We report on a prototype protocol for the automatic and fast construction of congruous sets of QM/MM models of rhodopsin-like photoreceptors and of their mutants. In the present implementation the information required for the construction of each model is essentially a crystallographic structure or a comparative model complemented with information on the protonation state of ionizable side chains and distributions of external counterions. Starting with such information, a model formed by a fixed environment system, a flexible cavity system, and a chromophore system is automatically generated. The results of the predicted vertical excitation energy for 27 different rhodopsins including vertebrate, invertebrate, and microbial pigments indicate that such basic models could be employed for predicting trends in spectral changes and/or correlate the spectral changes with structural variations in large sets of proteins.

Lake Baikal is the deepest and one of the most ancient lakes in the world. Its unique ecology has resulted in the colonization of a diversity of depth habitats by a unique fauna that includes a group of teleost fish of the sub-order Cottoidei. This relatively recent radiation of cottoid fishes shows a gradual blue-shift in the wavelength of the absorption maximum of their visual pigments with increasing habitat depth. Here we combine homology modeling and quantum chemical calculations with experimental in vitro measurements of rhodopsins to investigate dim-light adaptation. The calculations, which were able to reproduce the trend of observed absorption maxima in both A1 and A2 rhodopsins, reveal a Barlow-type relationship between the absorption maxima and the thermal isomerization rate suggesting a link between the observed blue-shift and a thermal noise decrease. A Nakanishi point-charge analysis of the electrostatic effects of non-conserved and conserved amino acid residues surrounding the rhodopsin chromophore identified both close and distant sites affecting simultaneously spectral tuning and visual sensitivity. We propose that natural variation at these sites modulate both the thermal noise and spectral shifting in Baikal cottoid visual pigments resulting in adaptations that enable vision in deep water light environments.

Intermolecular forces and energies are not directly observable and cannot be retrieved from a crystal structure determination, which simply pictures the resulting equilibrium between forces. In this work, using compression to sample the repulsive part of potentials, we show that high pressure studies may give insight in the nature of intermolecular forces. We focus our attention on controversial π*←−n interactions between NO 2 groups, which exhibit several conformations. Using XRD and ab initio calculations, we describe the high pressure behavior and phase transition of 4-amino-4 -nitrobiphenyl. To deepen our understanding on the nature of NO 2 • • • NO 2 interactions we used several theoretical tools, including pairwise atomic potential energies and forces. The results show that this interaction is associated with a mild stabilization. Since the repulsive forces are experimentally found to be weaker than those of other contacts, we conclude that also the attractive forces are weak, although in excess of the repulsive ones.

We outline in this combined experimental and theoretical NMR study that sign and magnitude of J(Si,H) coupling constants provide reliable indicators to evaluate the extent of the oxidative addition of Si-H bonds in hydrosilane complexes. In combination with experimental electron density studies and MO analyses a simple structure-property relationship emerges: positive J(Si,H) coupling constants are observed in cases where M → L π-back-donation (M = transition metal; L = hydrosilane ligand) dominates. The corresponding complexes are located close to the terminus of the respective oxidative addition trajectory. In contrast negative J(Si,H) values signal the predominance of significant covalent Si-H interactions and the according complexes reside at an earlier stage of the oxidative addition reaction pathway. Hence, in nonclassical hydrosilane complexes such as CpTi(PMe)(HSiMeCl) (with n = 1-3) the sign of J(Si,H) changes from minus to plus with increasing number of chloro substituents n and maps the rising degree of oxidative addition. Accordingly, the sign and magnitude of J(Si,H) coupling constants can be employed to identify and characterize nonclassical hydrosilane species also in solution. These NMR studies might therefore help to reveal the salient control parameters of the Si-H bond activation process in transition-metal hydrosilane complexes which represent key intermediates for numerous metal-catalyzed Si-H bond activation processes. Furthermore, experimental high-resolution and high-pressure X-ray diffraction studies were undertaken to explore the close relationship between the topology of the electron density displayed by the η(Si-H)M units and their respective J(Si,H) couplings.

The ever-increasing attention on environmental problems and sustainability has highlighted several problems related to the use of conventional pesticides in the agricultural industry, e.g., toxic residues in the soil and hazards to the environment and human health. In the search for natural antimicrobial and insecticide alternatives, essential oils (EOs) and their active components have emerged as promising candidates, but they suffer from some drawbacks related to their physical properties. We exploited cocrystallization with isonicotinamide, pyrazine, 2,3,5,6-tetramethylpyrazine, and 2,3-dimethylquinoxaline as a workaround to extend the applicability of carvacrol and thymol as natural pesticides, improving their ambient delivery profile. The cocrystals were prepared mechanochemically in a green solvent-free manner, and their purity, structure, and stability were investigated via powder and single-crystal X-ray diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and density functional theory (DFT) calculations. Moreover, each cocrystal was also tested in terms of EO release by headspace–gas chromatography–mass spectrometry (GC–MS) analysis over 14 days. We also report the conversion of a cocrystal to a new structure with different stoichiometry, which seems to afford a delayed boost of EO release that could be very interesting for food preservation applications.