Essential dynamics for the study of microstructures in liquids

Abstract

Essential Dynamics (ED) is a powerful tool for analyzing molecular dynamics (MD) simulations and it is widely adopted for conformational analysis of large molecular systems such as, for example, proteins and nucleic acids. In this study, we extend the use of ED to the study of clusters of arbitrary size constituted by weakly interacting particles, for example, atomic clusters and supramolecular systems. The key feature of the method we present is the identification of the relevant atomic-molecular clusters to be analyzed by ED for extracting the information of interest. The application of this computational approach allows a straightforward and unbiased conformational study of the local microstructures in liquids, as emerged from semiclassical MD simulations. The good performance of the method is demonstrated by calculating typical observables of liquid water, that is, NMR, NEXAFS O1s, and IR spectra, known to be rather sensitive both to the presence and to the conformational features of hydrogen-bonded clusters.

Crabrolin, a natural antimicrobial peptide: structural properties

“…the peptide polarity; (iii) the hydrophobic and hydrophilic solvent‐accessible surfaces as provided by standard criteria ; and (iv) an estimation of the peptide volume and shape. This latter quantity has been accomplished by using a recently proposed method based on elementary mechanics and here only briefly outlined.…”

Exploring the role of L209 residue in the active site of NDM-1 a metallo-β-lactamase

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