Visualization of solvation structures in liquid mixtures

• Published in: Journal of molecular graphics & modelling 1997-10, Vol.15 (5), p.301-306
• Main Authors: Bergman, Dan L, Laaksonen, Leif, Laaksonen, Aatto
• Format: Article
• Language: English
• Subjects: 3D solvation structure; Computer Graphics; Computer Simulation; MD simulation; Models, Chemical; Models, Molecular; Oxygen - chemistry; Software; Solutions; spatial distribution function; Static Electricity; Water - chemistry; water–acetonitrile mixture
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/S1093-3263(98)00003-5

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.