The editor is started by clicking on a molecule entry from the table below. You can view the structure, edit it if necessary, and subsequently submit it for calculation.
You will get a webpage with the starting structure in a Jmol applet.
Click on an atom, select a substituent from the drop-down list, and
confirm the change with the Replace button.
When you are done, click the calculate! button to start the calculation.
If you know how to manipulate a z-matrix, you can also edit the file directly and confirm it with the "apply" button.
The Suggestions...-links point to pages that give examples of exercises.
These mention substituents to introduce, and to what purpose.
Some instructions appear in a separate, small window, to keep next to your editing
and calculating work in the main window. In other cases the links point to pages that
are part of a subject listed on the Mol4D tutorials page.
NEW! All just a few clicks away!
Define your own reaction path! Starting from one of the
structures at the bottom, introduce substituents, and define one or two
variables to be changed systematically. This results in an animated
structure and a clickable energy diagram, either a curve or a grid.
The first series of compounds have built-in instructions to perform a certain conformational change, or reaction. No buttons to change these will be shown. | |||
| Subject & Link to editor | Suggestions for exercises | ||
| Rotation around central bond in ethane | Substituents to add | ||
| in steps of 30° (faster) | using Jmol | ||
| in steps of 10° (smoother plot) | using Jmol | ||
| SN2 reactions | Viewing orbitals
Limitations | ||
| reaction of chloride anion with methyl bromide | Jmol | ||
| reaction with 2-bromopropane | Jmol | ||
| reaction with 2-bromobutane | Jmol | ||
| Nitrogen inversion in dimethyl amine | Jmol | Open vs. ring structure | |
| Nitrogen inversion in N-methylaziridine | Jmol | ||
| Oxirane, effects of substituents | Jmol | Acid catalyzed ring opening | |
| Diels-Alder reaction |
Substituted transition states
HOMO/LUMO coefficients |
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| Carbanion next to carbonyl, delocalized or not? Calculate and display the HOMO |
Look at the MO pictures | ||
| In norbornanone methylene anion | Jmol | ||
| In norbornanone bridgehead anion | Jmol | ||
| Electrophilic aromatic substitution | More about this subject . . | ||
| Benzenonium ion C6H7+ | Jmol | ||
| Benzyl cation C7H7+ | Jmol | ||
| Nitration of benzene | Jmol | ||
| Compare two benzenonium ions | Jmol |
Enter one substituent to examine its effect; or a substituent para in one ring, meta in the other. Compare the energies of the first and the last structure in the animation. |
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| Compare stability of two benzyl cations | Jmol | ||
Grid calculations to locate transition state | |||
These entries have been moved to a separate page | |||
The compounds below appear in a more flexible editor environment. Apart from simple editing and minimizing the structure, extar buttons allow for the identification of bonds to rotate, or to change in length. | ||
| new: nomenclature test | new: stereo editor, an R/S exercise | |
| templates for constructing (not minimizing) metal complexes | ||
| square planar | octahedral | |
Some animations can not be obtained from one single calculation. A number of xyz-files resulting from a combination of calculations can be found on our xyz-files page.