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Publication Metadata only Influence of hydrogen bond on the mesomorphic behaviour in urethane based liquid crystalline compounds: experimental and computer simulation study(Elsevier, 2020) Korkmaz, Burak; Agtas, Sinem; Sutay, Berkay; Yıldırım, Erol; Yurtsever, Mine; Senkal, B. Filiz; Gürsel, Yeşim; Department of Chemistry; Yılgör, İskender; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; 24181We present a combined experimental and theoretical study on the novel hydrogen-bonded liquid crystalline complex (UR-LC11) exhibiting both nematic and smectic phases upon cooling. The complex was prepared by mixing 2-(2-methoxyethoxy)ethylbutyl carbamate (UR) as H-bond acceptor with calamitic mesogen 4 '-((11-hydroxyundecyl)oxy)-[1,1 '-biphenyl]-4-carbonitrile (LC11) as H-bond donor. The complex was characterized by FTIR technique and its liquid crystalline properties were studied by differential scanning calorimetry (DSC) and polarized optical microscope (POM). The experimental IR spectra were compared with theoretically obtained IR spectra by Density Functional Theory (DFT) to suggest the structure of hydrogen-bonded liquid crystal (LC). The molecular dynamics (MD) simulationswere performed to understand the impact of hydrogen bonding on the mesomorphic behaviour of the complex and the temperature dependency of the transitions between the mesophases. We determined that UR-LC11 is a stable H-bond acceptor/donor type complex and a single H-bond forms between the carbonyl oxygen atom of the amidemoiety of UR and the hydrogen atomof the terminal hydroxyl group of the LC11. Although LC11 is present only in nematic liquid crystalline form, the new complex displayed both nematic and smectic phases during cooling. The reason for the two distinctive LC phases was explained by the presence of hydrogen bond interactions, which provides structural flexibility. Besides, H-bond maintains uniaxial rod shape of the molecule to promote self-assembly behaviour and induces positional ordering in the smectic phase. The enhancement in the self-assembly of the H-bonded chains in the complex is reflected in the increased.Hfusion values. Due to the intermolecular p-p interactions of the phenyl rings and the formation of strong dipoles on the backbone, especially at the cyanobiphenyl end of the chains, the longrange directional order of the dipoles along their long axes are preserved at elevated temperatures and nematic to isotropic phase transition is observed at around 370 K both experimentally and theoretically.Publication Open Access Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses(American Institute of Physics (AIP) Publishing, 1993) Space B.; Rabitz H.; Department of Mathematics; Aşkar, Attila; Faculty Member; Department of Mathematics; College of Sciences; 178822A subspace dynamics method is presented to model long time dynamical events. The method involves determining a set of vectors that span the subspace of the long time dynamics. Specifically, the vectors correspond to real and imaginary low frequency normal modes of the condensed phase system. Most importantly, the normal mode derived vectors are only used to define the subspace of low frequency motions, and the actual time dependent dynamics is fully anhannonic. The resultant projected set of Newton's equations is numerically solved for the subspace motions. Displacements along the coordinates outside the subspace are then constrained during the integration of the equations of motion in the reduced dimensional space. The method is different from traditional constraint methods in that it can systematically deduce and remove both local and collective high frequency motions of the condensed phase system with no a priori assumptions. The technique is well suited to removing large numbers of degrees of freedom, while only keeping the very low frequency global motions. The method is applied to highly anhannonic Lennard-Jones crystal and glass systems. Even in these systems with no intramolecular degrees of freedom or obvious separation of time scales, the subspace dynamics provides a speed up of approximately a factor of 5 over traditional molecular dynamics through use of a larger integration time step. In the cases illustrated here a single set of subspace vectors was adequate over the full time interval, although this is not expected to be true for all systems.Publication Metadata only The entry of molecular species into the lattice of an electroactive polymer during its dissolution(Elsevier Science Bv, 2006) Morton Blake, D. A.; Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129Molecular details obtained from quantum chemical DFT calculations on 3-methylthiophene oligomers are used in a molecular dynamics (MD) investigation of the solution-interface region of the soluble polymer poly(3-alkylthiophene) in its oxidized (electroactive) form. The MD shows that the presence of the solvent interface results in conformational changes in the polymer main chains in that region from all-trans to largely cis. The entry of BF4- ions and solvent molecules (chloroform) across the interface from the solvent to the positively charged polymer is anisotropic (particularly for the ions), entry occurring most readily along the direction of the main chains. Both BF4- solute ions and CHCl3 solvent molecules occupy specific sites in the polymer, but those of the BF4- ions are the better defined. A temperature study of the incursion of the two species into the polymer shows that the entry of the ions has a small activation energy.