PMID: 9640561Jun 26, 1998Paper

Visualization of solvation structures in liquid mixtures

Journal of Molecular Graphics & Modelling
D L BergmanA Laaksonen

Abstract

Spatial distribution functions of atomic densities. SDFs, have been proposed as a natural starting point for analysis of local molecular structure in liquids and solutions. The local structure in these systems is often complex and this is reflected in the fact that SDFs can be difficult to visualize. Among the different methods that can be used to visualize SDFs we discuss 3D isodensity surfaces, cross-sections, and 'comic book' animations. We also discuss the possibility of a simultaneous visualization of SDFs and other 3D fields, such as the electron density. These techniques are all intended to emphasize and bring out aspects of SDFs that promote a further understanding of the local molecular structure. OpenGL-based software has been used under X-Windows to implement these techniques, and we argue that high-quality molecular graphics need not be expensive. Data from a molecular dynamics simulation of an equimolar binary mixture of water and acetonitrile have been used to illustrate the discussion.

References

Mar 1, 1992·Journal of Molecular Graphics·L Laaksonen

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Citations

May 2, 2008·Journal of Molecular Modeling·Arjen-Joachim JakobiTimothy Clark
Nov 18, 2005·Journal of Computer-aided Molecular Design·Laurence LeherteDaniel P Vercauteren
Jun 14, 2005·Il Farmaco·Roberto ArtaliAntonio Del Pra
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Jun 25, 2010·Journal of the American Chemical Society·Matthew D LiptakKara L Bren
Jun 20, 2012·Journal of the American Chemical Society·Samuel A WilsonEdward I Solomon
Dec 25, 2012·Journal of the American Chemical Society·Samuel A WilsonEdward I Solomon
Aug 21, 2008·Journal of the American Chemical Society·Timothy A JacksonLawrence Que
Mar 21, 2009·The Journal of Physical Chemistry. B·Matthew D LiptakThomas C Brunold
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