Molecular features contributing to the lower viscosity of phosphonium based ionic liquids (ILs) compared to ammonium based ILs are investigated by static quantum chemistry calculations and classical molecular dynamics simulations. The larger bond distance and the higher flexibility of bond angles and dihedral angles in the phosphonium compounds tend to reduce their viscosity compared to ammonium analogues, while the strongly localized charge at the central atom has the opposite effect. Fast translational ion dynamics is also found to be related to a short counter-ion association lifetime in the investigated compounds. Furthermore, a weak structuring between the center of charges also seems to increase mobility. Interestingly, the order of ion pair interaction energies in the gas phase is reversed compared to the order of counter-ion association lifetimes in the liquid, which highlights the important role of solvation in ILs. Overall, the higher flexibility of the bond and dihedral angles of the phosphonium compounds appears to be the most important factor in producing the lower viscosity of these ILs compared to their ammonium analogues.

We investigated the red absorbing, dark stable state (Pr state) of the second GAF domain of the cyanobacteriochrome AnPixJ (AnPixJg2) by a molecular dynamics simulation of 1 μs duration. Our results reveal two distinct conformational isoforms of the chromophore, from which only one was known from crystallographic experiments. The interconversion between both isoforms is accompanied by alterations in the hydrogen bond pattern between the chromophore and the protein and the solvation structure of the chromophore binding pocket. The existence of sub-states in the Pr form of AnPixJg2 is supported by the results from experimental C MAS NMR spectroscopy. Our finding is consistent with the observation of structural heterogeneity in other cyanobacteriochromes and phytochromes.

We present electronic structure theory calculations and scanning tunneling microscopy experiments for the adsorption of α-sexithiophene on the 100 surface of gold. Our density-functional theory calculations show that α-sexithiophene prefers to adjust an energetically unfavorable adsorption site by modifying the gold surface over seeking out more favorable adsorption sites. Molecular adsorption results in a complex charge transfer pattern, with more charge transfer in more stable sites. Our results challenge the current paradigm that weakly interacting (e.g., physisorbed) molecules perceive metal surfaces as rigid templates with preordained adsorption sites.

We investigate domain formation and local morphology of thin films of α-sexithiophene (α-6T) on Au(100) beyond monolayer coverage by combining high resolution scanning tunneling microscopy (STM) experiments with electronic structure theory calculations and computational structure search. We report a layerwise growth of highly-ordered enantiopure domains. For the second and third layer, we show that the molecular orbitals of individual α-6T molecules can be well resolved by STM, providing access to detailed information on the molecular orientation. We find that already in the second layer the molecules abandon the flat adsorption structure of the monolayer and adopt a tilted conformation. Although the observed tilted arrangement resembles the orientation of α-6T in the bulk, the observed morphology does not yet correspond to a well-defined surface of the α-6T bulk structure. A similar behavior is found for the third layer indicating a growth mechanism where the bulk structure is gradually adopted over several layers. arXiv:2003.07771v1 [cond-mat.mtrl-sci]