The scene shown on C&EN's cover this week is one view of an interactive VRML (virtual reality modeling language) model showing close intermolecular interactions between an oxygen atom in a crystal structure and a C - H hydrogen of a chlorinated aromatic system.
The VRML model was created by researchers Christopher S. Page and Omer Casher in the department of chemistry at Imperial College of Science, Technology & Medicine, London. Page and Casher are in the group headed by Henry S. Rzepa, a reader in organic chemistry at Imperial College. The view was captured in Cosmo Player, a VRML web browser plug-in viewer from Silicon Graphics Inc., Mountain View, Calif. The objects along the bottom of the scene are Cosmo Player's navigation tools.
Page explains that the image was a composite of two types of information. The saturnian-ring effect results from a semiempirical quantum mechanical calculation and represents the interaction energy between chlorobenzene and a water molecule lying in the plane of the ring as a function of the relative position of the water molecule. The surroundi ng sphere of blue dots represents the positions of oxygen atoms relative to a chlorobenzene moiety arising from a search of the Cambridge Crystallographic Database for contacts that come within 5.0 Å of the ring center. Special attention is drawn to close contacts (less than 2.5 Å) with aryl hydrogens by using dots colored red.
The image, Page explains, was generated using essentially prototype methods, the software for which was described in a paper presented at the 2nd Electronic Conference on Computational Chemistry held on the World Wide Web a year ago.
More recent work has resulted in the image above. In this image, the interaction energy represented by the saturnian ring has been replaced by an electrostatic potential surface represented by the aqua cloud that was computed at a much higher level of theory. Page points out that the electrostatic potential reveals subtle differences in hydrog en bonding capability between the ortho, meta, and para hydrogens that are not visible in the computation for the cover image.
In the image shown here, the dots have been replaced by arrows. Page explains that the arrows, unlike the dots, give information about the orientation of the interacting group. Such information is very useful in determining whether the interactions are hydrogen bonding or merely a consequence of other factors such as crystal-packing forces, since it gives at least some idea of the lone-pair directionality. The arrows have been colored according to the functional group so that the diagram differentiates between them.
One aspect of the diagram relates to so-called data mining, and Casher explains that the scatter plots using dots or arrows are examples of how VRML can be used effectively for doing this in a chemical context. In this case, the complete results of a database query are contained in one 3-D model within a web browser, something Casher describes as a paradigm shift in the retrieval of chemical structure data. Through the hyperlinking of various components of the 3-D model, such as the dots or arrows, users can probe the data further to examine, for instance, VRML models of crystal structures along with corresponding literature references encoded in HTML (hypertext markup language).
