Accurate modeling of molecular crystal through dispersion-corrected density functional theory (DFT-D) method
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Accurate modeling of molecular crystal through dispersion-corrected density functional theory (DFT-D) method Bohdan Schatschneider1, Jian-jie Liang2* 1 The Pennsylvania State University, Fayette-The Eberly Campus 2 Accelrys, Inc., 10188 Telesis Court, Suite 100 San Diego, CA 92121 USA ABSTRACT Crystal structure, pressure response, and polymorph transformation were investigated for crystalline indole through dispersion-corrected density functional theory (DFT-D) method. An accurate, nonempirical method (as in the latest implementations of CASTEP ) is used to correct for the general DFT scheme to include van der Waals interactions important in molecular crystals. Ambient structural details, including space group symmetry, density, and fine structural details, such as bicyclic angles, have been reproduced to within experimental accuracy. Pressure response of the structure was obtained to isostatic pressure up to 25 GPa, in increments of 1 GPa. Evolution of space group symmetry and the bicyclic angle were mapped as a function of pressure. A previously unknown phase transformation has been identified around 14 GPa of isostatic pressure. Total energies of the phases before and after phase transformation are nearly identical, with a phase transformation barrier of 0.9 eV. The study opens up the door to reliable DFT investigations of chemical reactions of crystalline aromatic systems under high pressure (e.g. formation of amorphous sp3 hybridized phases). INTRODUCTION Indole is a vital heterocyclic aromatic compound indirectly involved in many biological processes such as neurotransmission (serotonin), sleep/wake cycles (melatonin) and skin irradiation protection (melanin). Its crystalline form assembles the individual molecules in an orthorhombic herringbone (HB) motif within large platelets, with the long molecular axis essentially aligned along the c unit cell parameter [1]. Indole, being a molecular crystal, falls under the class of “soft solids” [2] which are characterized by two sets of interactions, intramolecular and intermolecular. There are considerable strength differences between intramolecular and intermolecular forces with the former being ~42 times as strong as the latter [3]. The molecular stability of indole can be attributed to the strong intramolecular forces which hold the covalent interactions together while the weaker intermolecular van der Waals interactions allow for the high compressibility of the solid. It has been proposed that as pressure is increased, intermolecular voids become smaller and the intermolecular forces become increasingly repulsive [2]. The increased repulsive
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behavior between molecules in turn affects the internal bonds, causing them to become unstable, resulting in chemical changes on a molecular level. The process of increased repulsion followed by chemical instability is how sp3 amorphous products are produced in PAH’s. However, before the pressure is sufficiently high to alter intramolecular interactions and force chemical transformations to occur, the crystal structure
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