Effect of water on the structure of a prototype ionic liquid

2016 ◽  
Vol 18 (34) ◽  
pp. 23474-23481 ◽  
Author(s):  
Oleg Borodin ◽  
David L. Price ◽  
Bachir Aoun ◽  
Miguel A. González ◽  
Justin B. Hooper ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Md Simulations ◽  
High Energy ◽  
X Ray Diffraction ◽  
X Ray ◽  
Effect Of Water ◽  
Influence Of Water

The influence of water on the structure of a prototype ionic liquid (IL) 1-octyl-3-methylimidazolium tetrafluoroborate (C8mimBF4) is examined in the IL-rich regime using high-energy X-ray diffraction (HEXRD) and molecular dynamics (MD) simulations.

scholarly journals Molecular Dynamics Modellization and Simulation of Water Diffusion through Plant Cutin

1999 ◽  
Vol 54 (11) ◽  
pp. 896-902 ◽  
Author(s):  
Antonio Matas ◽  
Antonio Heredia
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Structural Information ◽  
Md Simulations ◽  
Water Molecules ◽  
Plant Cuticle ◽  
X Ray Diffraction ◽  
Cross Link ◽  
X Ray ◽  
Good Agreement

Abstract A theoretical molecular modelling study has been conducted for cutin, the biopolyester that forms the main structural component of the plant cuticle. Molecular dynamics (MD) simulations, extended over several ten picoseconds, suggests that cutin is a moderately flexible netting with motional constraints mainly located at the cross-link sites of functional ester groups. This study also gives structural information essentially in accordance with previously reported experimental data, obtained from X -ray diffraction and nuclear magnetic resonance experiments. MD calculations were also performed to simulate the diffusion of water mole­cules through the cutin biopolymer. The theoretical analysis gives evidence that water perme­ation proceedes by a “hopping mechanism”. Coefficients for the diffusion of the water molecules in cutin were obtained from their mean-square displacements yielding values in good agreement with experimental data.

scholarly journals Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein

2019 ◽  
Author(s):  
David C. Wych ◽  
James S. Fraser ◽  
David L. Mobley ◽  
Michael E. Wall
Keyword(s):  
Molecular Dynamics ◽  
Rigid Body ◽  
Diffraction Data ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atom Pairs ◽  
Collective Motions ◽  
Rigid Body Motions ◽  
Insight Into

AbstractTo gain insight into crystalline protein dynamics, we performed molecular-dynamics (MD) simulations of a periodic 2×2×2 supercell of staphylococcal nuclease. We used the resulting MD trajectories to simulate X-ray diffraction and to study collective motions. The agreement of simulated X-ray diffraction with the data is comparable to previous MD simulation studies. We studied collective motions by analyzing statistically the covariance of alpha-carbon position displacements. The covariance decreases exponentially with the distance between atoms, which is consistent with a liquid-like motions (LLM) model, in which the protein behaves like a soft material. To gain finer insight into the collective motions, we examined the covariance behavior within a protein molecule (intra-protein) and between different protein molecules (inter-protein). The inter-protein atom pairs, which dominate the overall statistics, exhibit LLM behavior; however, the intra-protein pairs exhibit behavior that is consistent with a superposition of LLM and rigid-body motions (RBM). Our results indicate that LLM behavior of global dynamics is present in MD simulations of a protein crystal. They also show that RBM behavior is detectable in the simulations but that it is subsumed by the LLM behavior. Finally the results provide clues about how correlated motions of atom pairs both within and across proteins might manifest in diffraction data. Overall our findings increase our understanding of the connection between molecular motions and diffraction data, and therefore advance efforts to extract information about functionally important motions from crystallography experiments.

scholarly journals Spontaneous self-assembly and structure of perfluoroalkylalkane surfactant hemimicelles by molecular dynamics simulations

2019 ◽  
Vol 116 (30) ◽  
pp. 14868-14873 ◽  
Author(s):  
Gonçalo M. C. Silva ◽  
Pedro Morgado ◽  
Pedro Lourenço ◽  
Michel Goldmann ◽  
Eduardo J. M. Filipe
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Md Simulation ◽  
Grazing Incidence ◽  
Md Simulations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Spontaneous Formation ◽  
Rational Explanation ◽  
Dynamics Simulations

Fully atomistic molecular-dynamics (MD) simulations of perfluoroalkylalkane molecules at the surface of water show the spontaneous formation of aggregates whose size and topography closely resemble the experimentally observed hemimicelles for this system. Furthermore, the grazing incidence X-ray diffraction (GIXD) pattern calculated from the simulation trajectories reproduces the experimental GIXD spectra previously obtained, fully validating the MD simulation results. The detailed analysis of the internal structure of the aggregates obtained by the MD simulations supports a definite rational explanation for the spontaneous formation, stability, size, and shape of perfluoroalkylalkane hemimicelles at the surface of water.

Solvation Structure of Poly(ethylene glycol) in Ionic Liquids Studied by High-energy X-ray Diffraction and Molecular Dynamics Simulations

2013 ◽  
Vol 46 (6) ◽  
pp. 2369-2375 ◽  
Author(s):  
Hanako Asai ◽  
Kenta Fujii ◽  
Kengo Nishi ◽  
Takamasa Sakai ◽  
Koji Ohara ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquids ◽  
Ethylene Glycol ◽  
High Energy ◽  
X Ray Diffraction ◽  
Poly Ethylene Glycol ◽  
X Ray ◽  
Solvation Structure ◽  
Poly Ethylene ◽  
Dynamics Simulations
Sign in / Sign up

Export Citation Format

Share Document