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. � 2014 Wiley Periodicals, Inc.

Essential dynamics for the study of microstructures in liquids

STENER, MAURO;
2015

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. � 2014 Wiley Periodicals, Inc.
File in questo prodotto:
File Dimensione Formato  
Essential dynamics for the study of microstructures in liquids.pdf

non disponibili

Descrizione: pdf articolo pubblicato
Tipologia: Documento in Versione Editoriale
Licenza: Digital Rights Management non definito
Dimensione 718.99 kB
Formato Adobe PDF
718.99 kB Adobe PDF   Visualizza/Apri   Richiedi una copia
essential - supplementary informations.pdf

non disponibili

Descrizione: pdf supplementary informations
Tipologia: Altro materiale allegato
Licenza: Digital Rights Management non definito
Dimensione 160.17 kB
Formato Adobe PDF
160.17 kB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11368/2832418
Citazioni
  • ???jsp.display-item.citation.pmc??? 2
  • Scopus 12
  • ???jsp.display-item.citation.isi??? 12
social impact