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Mol4D (Molecules in Four Dimensions) is a Web-based molecule editor
using the Chime browser plug-in linked to a MOPAC calculation engine
that yields structural data (geometry parameters, transition states) as
well as electronic data (orbitals, electrostatic potential).
Visualization and interactivity are the predominant features. Students
can submit and obtain computational results within seconds using their
Internet browser. The structure and the keywords used as input for the
computation can be chosen and amended using a menu interface. Among the
options are the output of orbital information (in VRML format) and the
selection of parameters for a linear or grid scan. Results from the
computation are presented in a Web page that features an interactive
energy plot and animation, when applicable. The MDL Chime
plug-in (1) is widely used to display
three-dimensional structures in Web pages. Use of Chime is generally
confined to single structures, sometimes including buttons that offer
shortcuts to Chime functions. Chime animations based on the multiple
xyz-format, with control buttons to step through the animation, are not
widely used. Apart from the commonly used xyz, pdb, and mol2 files,
Chime also supports the MOPAC (2) input file
format based on a z-matrix of internal coordinates (distances, angles,
and dihedrals). This format allows for some molecule editing, in which
a hydrogen or other monovalent atom can be replaced by a predefined
group of atoms (for example, –CH3, –NO2,
–C6H5), resulting in a new structure.
Judicious use of this feature allows the construction of almost any
organic molecule. We have implemented this idea, taken from the MOLDEN
(3) z-matrix editor, with a series of CGI
scripts on our WWW server that also handle the input to MOPAC and the
presentation of the results. The Web page returned to the user (Figure
1) includes the Chime structure, the calculated heat of formation, and
buttons to allow geometrical measurements and control of the display of
the electrostatic potential surface. If orbital information is
requested, a link is included to our MOPAC-to-VRML service, which
produces a Web page from which the orbital number and other relevant
parameters can be selected.
 | | Figure 1. Result page for simple minimization. |
Another feature of Mol4D is the visualization of
reactions and conformational changes. Starting with a predefined input
file, students may add a group to a skeleton, run the calculation, and
study the substituent effect on the reaction or conformational change.
The Diels–Alder reaction is a typical example where this approach
is useful to study directive effects of substituents in butadiene and
ethylene, for instance. Comparison of the energy profiles and energy
data from the output pages allows determination of the favored
reaction. The result of a one-dimensional reaction (e.g., a
conformational change) coordinate calculation is presented with a
number of features (Figure 2). The Chime display, based on a
multiple-xyz file, is presented with buttons that control the animation
through the respective structures. The energy values are translated
into an interactive energy plot connected to the Chime display. This
connection links the structure animation to a red ball that moves along
the energy curve in the plot. In addition, clicking on a point in the
graph displays the corresponding structure as a Chime object. A
third display window includes the alphanumeric data (parameter
value, energy).
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| Figure 2. Result page for a one-dimensional reaction
(conformational change), which provides for animation of the
change. |
In the two-dimensional case the
result is an interactive grid plot with energy contour lines (Figure
3). In practice the grid calculation is often applied to locate a
transition state. Therefore, this feature has a couple of follow-up
links: recalculation of the grid with different starting values,
corresponding to zooming in on the transition state or shifting it; and
continuation with an IRC calculation from a selected structure close to
the saddle point (Figure 3). This latter link points to an automated
reaction animation service, described in detail in the following paper
(4). A cross in the plot marks the position
of a saddle point, and a line displays the direction of the reaction
coordinate at this point.
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| Figure 3. Starting point of the IRC calculation for a 2+3
cycloaddition of ethylnitrile oxide and ethylene. |
Supplemental Material
Examples of exercises for use with Mol4D are included in the
accompanying documentation.
Literature Cited
- Chime is a product of Molecular Design Ltd.
(accessed Mar 2003).
- MOPAC: Stewart, James J. P. J. Comput. Aided Mol. Design 1990, 4, 1–105.
- MOLDEN:
Schaftenaar, G.; Noordik, J. H. J. Comput. Aided Mol. Design
2000, 14, 123. (accessed Mar 2003).
- Stueker, O.; Brunberg, I.; Fels, G.; Borkent, H.:
van Rooij, J. J. Chem. Educ.
2003, 80, 583.
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