Validating a Strategy for Molecular Dynamics Simulations of Cyclodextrin Inclusion Complexes through Single-Crystal X-ray and NMR Experimental Data: A Case Study

2009 ◽  
Vol 113 (27) ◽  
pp. 9110-9122 ◽  
Author(s):  
Giuseppina Raffaini ◽  
Fabio Ganazzoli ◽  
Luciana Malpezzi ◽  
Claudio Fuganti ◽  
Giovanni Fronza ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Single Crystal ◽  
Molecular Dynamics Simulations ◽  
Inclusion Complexes ◽  
X Ray ◽  
Cyclodextrin Inclusion Complexes ◽  
Cyclodextrin Inclusion ◽  
Dynamics Simulations

scholarly journals Crystal structure of Ag-exchanged levyne intergrown with erionite: Single-crystal X-ray diffraction and Molecular Dynamics simulations

2020 ◽  
Vol 105 (11) ◽  
pp. 1631-1638 ◽  
Author(s):  
Georgia Cametti ◽  
Sergey V. Churakov
Keyword(s):  
Molecular Dynamics ◽  
Single Crystal ◽  
Molecular Dynamics Simulations ◽  
Exchange Process ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Threefold Axis ◽  
Space Group ◽  
X Ray ◽  
Dynamics Simulations

Abstract The modification of natural zeolites via ion exchange is an efficient technique used to improve their performances and tune their properties for specific applications. In this study, a natural levyne-Ca intergrown with erionite was fully exchanged by Ag+ and its structure [with idealized chemical composition Ag6(Si,Al)18O36·18H2O] was investigated by combining a theoretical and experimental approach. Single-crystal X-ray diffraction data demonstrated that Ag-levyne maintained the R3m space group, characteristic of the natural levyne. Ag ions distribute over partially occupied sites along the threefold axis and, differently from the pristine material, at the wall of the 8-membered ring window of the lev cavity. The lack of ~30% of Ag ions that could not be located by the structural refinement is ascribed to the strong disorder of the extraframework occupants. The structural results obtained by Molecular Dynamics simulations are in overall agreement with the experimental data and showed that, on average, Ag+ is surrounded by ~2 H2O and 1 framework oxygen at distances between 2.43 and 2.6 Å. Molecular Dynamics trajectories indicate that the occurrence of silver inside the D6R cage depends on the water content: silver occupancy of D6R cages is estimated to be 83, 30, and 0% when the structure contains 3, 2.5, and 2 H2O per Ag ion, respectively. The cation-exchange process, as demonstrated by scanning electron microscopy and energy-dispersive spectroscopy (SEM-EDS) spectrometry, affects the intergrown erionite as well. A structural characterization of the Ag-erionite phase (with dimension <100 μm) was possible by means of a CuKα micro-focus source: structure solution pointed to P63/mmc space group, indicating no change with respect to natural erionite. In agreement with previous studies, K ions in the cancrinite cage could not be exchanged, whereas Ag+ is found in the eri cavity.

scholarly journals Local Structuring of Diketopyrrolopyrrole (DPP)-based Oligomers from Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Maryam Reisjalali ◽  
J. Javier Burgos-Marmol ◽  
Rex Manurung ◽  
Alessandro Troisi
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Mobility ◽  
Semiconducting Polymers ◽  
Microscopic Structure ◽  
Dynamics Simulations

The microscopic structure of high mobility semiconducting polymers is known to be essential for their performance but it cannot be easily deduced from the available experimental data. A series of...

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

Sign in / Sign up

Export Citation Format

Share Document