A Novel Conformational Searching Technique applied to small polymer units of 3-phenyl-1-ureidonitrile
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A Novel Conformational Searching Technique applied to small polymer units of 3-phenyl-1-ureidonitrile Ari Silver and Karl Sohlberg* Department of Chemistry Drexel University Philadelphia, PA 19104 ABSTRACT A novel conformational searching scheme is employed to identify low energy structures for low-degree polymers of 3-phenyl-1-ureidonitrile, a proposed thin film data storage material. Vibrational analysis of the predicted polymer structures is consistent with experimental reports and supports the experimentally proposed polymerization mechanism. INTRODUCTION In recent years, organic thin films have received increasing attention as a potential ultrahighdensity data storage media [1 - 4]. Thin films have been created that can store in excess of 1013 bits/cm2 [1], over 1 million times the density of a typical compact disc. Thin film technology has the potential to revolutionize data storage, but significant (technical) hurdles remain. Some films may not be stable over long periods of time [5,6], while for other films, the erasing process has not been demonstrated [1,3,4]. In order to design better films, it would be desirable to carry out theoretical modeling of the film material so that refinements in the material could be assisted by theoretical calculations. Here we present a physically motivated scheme to identify low energy structures of polymeric molecules and employ it to confirm the polymerization mechanism of 3phenyl-1-ureidonitrile (PUN). COMPUTATIONAL METHODS Conformational searching was carried out on the PUN molecule at several levels of polymerization. An exhaustive search was conducted on the monomer. A quasi-exhaustive search was conducted on the dimer (2-mer), and a novel searching scheme was used to treat the remainder of the PUN n-mers up through the 8-mer. The conformational searching was carried out with the MM+ Molecular Mechanics method [7]. The final optimized structures were refined by re-optimization with the semiempirical AM1 method [7]. All computations were carried out with the Hyperchem [7] computational chemistry package. Monomer Exhaustive Search. The PUN monomer was subject to an exhaustive search over the three dihedral angles denoted I, II and III in Figure 1. These three dihedral angles encompass the three single bonds in the molecule about which there is relatively free rotation. All three dihedral angles (see Figure 1) were iterated in 30° steps from –180° to 180° (13 steps). This yielded 133 (2197) trial starting structures. For each structure, a geometry
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optimization was performed using the MM+ method [7]. A Tool Command Language (TCL) script was written to automate the search through the Hyperchem -TCL interface. Dihedral Angle I: 5, 6, 7, 8 Dihedral Angle II: 6, 7, 8, 9 Dihedral Angle III: 7, 8, 9, 11 Figure 1. Structure of 3-phenyl-1-ureidonitrile. The exhaustive search yielded two stable conformers (local minima) of the PUN monomer. These conformers were subsequently re-optimized at the AM1 [7] level. A normal mode vibrational analysis on the optimized molecules
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