The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.
We examined the characteristics and behaviors of the carbon nanotube (CNT) and surfactants complexes in an aqueous environment using computational techniques to elucidate the effects of surfactants used to disperse the CNTs in toxicity studies of CNTs. We found that the cohesive energy per one adsorbed surfactant molecule of the CNTÀsurfactants complex depends on the type and the amount of the adsorbed surfactant molecules on the CNT surface. The CNTÀdipalmitoyl phosphatidylcoline (DPPC; a primary component of human lung surfactants) complex was more energetically stable than the CNTÀTween 80 (an artificial surfactant often used to disperse CNTs) complex by 20À60 kJ/mol. The average cohesive energy of the complexes was 330 kJ/mol. Such high cohesive energy suggests that the CNT molecule that was once covered by surfactant molecules is unlikely to return to its original bared form. Furthermore, we found that reactions of adsorption and desorption of surfactant molecules occur on the CNT surface in a time scale of milliseconds. Hence, the CNTs are thought to be coated by the "surfactant corona" composed of amphiphilic molecules, which is similar to a "protein corona" in the biological system. Moreover, CNTÀsurfactants complexes are believed to convert to some other more energetically stable CNTÀsurfactants complexes through a surfactant exchange due to the adsorption and desorption of surfactants on the CNT surface in the biological system. The specific surface area of the CNTs, which is one of the most important parameters for assessing the toxicity of a nanomaterial, is thought to change because of the surfactant exchange.
We theoretically investigate the energetically favorable orientation of poly(3-hexylthiophene) (P3HT) on self-assembled monolayers (SAMs) using molecular dynamics simulations. The effects of different kinds of SAMs are studied by examining a CH3-terminated SAM with a hydrophobic surface and an NH2-terminated SAM with a hydrophilic surface. We also investigate dynamic behavior of the systems with limited numbers of P3HT molecules on the SAM surfaces. The important factors in controlling the molecular orientation are elucidated from these results. We demonstrate that the edge-on orientation is more energetically favorable than the face-on orientation on both SAMs. On the other hand, the face-on orientation gains more intermolecular interaction energy between the P3HT molecules and the SAMs. This energy gain is larger in the NH2-terminated SAM than the CH3-terminated SAM. A limited number of P3HT molecules prefer to take the face-on orientation rather than the edge-on orientation. Our theoretical results suggest that the molecular orientation of P3HT is controllable by tuning the conditions of the film formation process and the intermolecular interactions between the P3HT molecules and SAMs.
We theoretically predict crystal structures and molecular arrangements for rubrene molecule using CONFLEX program and compare them with the experimental ones. The most, second-most, and fourth-most stable predicted crystal structures show good agreement with the triclinic, orthorhombic, and monoclinic polymorphs of rubrene, respectively. The change in molecular conformation is also predicted between crystalline and gas phases: the tetracene backbone takes flat conformation in crystalline phase as in the observed structure. Meanwhile, it is twisted in gas phase. The theoretical prediction method used in this work provides the successful results on the determination of the three kinds of crystal structures and molecular arrangements for rubrene molecule.
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