Click here to see an example of how to use the
molecule editor,
and a few notes on errors that might occur.
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 either Chime or Jmol.
Please note: the editor does not support all combinations of browsers and Chime versions.
Click on an atom, select a substituent from the drop-down list, and
confirm the change with the Apply 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.
Click here to see an example of how to use the
molecule editor,
and a few notes on errors that might occur.
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.
Note: not yet implemented in Jmol!
Moreover: if your calculation contains a point close to a transition state: with one click the structure is refined, and the reaction path to both the product and the reactant side is calculated! This Calculate and Animate a Reaction Path project is a joint exercise with Prof. Fels, University of Paderborn, Germany.
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 Chime | using Jmol | |
| in steps of 10° (smoother plot) | using Chime | using Jmol | |
| side chain rotamers in alpha helix | |||
| SN2 reactions | Viewing orbitals
Limitations | ||
| reaction of chloride anion with methyl bromide | Chime | Jmol | |
| reaction with 2-bromopropane | Chime | Jmol | |
| reaction with 2-bromobutane | Chime | Jmol | |
| Nitrogen inversion in trimethyl amine | Chime | Jmol | Open vs. ring structure |
| Nitrogen inversion in N-methylaziridine | Chime | Jmol | |
| Oxirane, effects of substituents | Chime | 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? |
Look at the MO pictures |
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| Electrophilic aromatic substitution | More on these 4 subjects . . |
| Compare acidity of carboxylic acids | |
Grid calculations to locate transition state, followed by IRC calculation to obtain reaction path | |
These entries have been moved to the CARP (Calculate and Animate a Reaction Path) page | |
Simple molecules, as starting points, using ChimeThe following compounds appear in a more flexible editor environment. Apart from simple editing and minimizing the structure, extra buttons allow for the identification of bonds to rotate, or to change in length. | ||
Same molecules, for use in JmolWorks the same as in Chime, apart from the 'set reaction path' option. | ||
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.