Intermolecular potential energy surfaces for the interaction between H 2 X (X O, S) and a metastable Ne * ( 3 P 2,0 ) atom

Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations

Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.

Measurements of Ionization Cross Sections by Molecular Beam Experiments: Information Content on the Imaginary Part of the Optical Potential

In this work, we present and analyze in detail new and recent ionization cross section and mass spectrum determinations, collected in the case of He*, Ne*-H2O, -H2S, and -NH3 ionizing collisions. These sets of data, obtained under the same experimental conditions, are relevant to identify differences in the autoionization stereodynamics of the three hydrogenated molecules and on the selective role of the imaginary part of the optical potential. We demonstrate that in these autoionization processes hydrogen and halogen bonds are competing because they are controlling both real and imaginary components of the optical potential that drives the complete reaction dynamics. In particular, we found that both components critically depend on the angular and radial approach between the reagent partners in determining the collision dynamics.