Help File and Information

Dates and Features

About the Calculation

All spectrum data and normal modes values are calculated by the quantum-mechanical program VAMP (semi-emprical method PM3). Because intensity peaks calculated by semi-empirical calculations are represented at to high wavenumbers, we have added a corection factor of 0.98 in this service. Although we have added this scoring factor, C=O bonds still are occurring at to high wavenumbers. Therefore, we have added another scoring factor (0.9) within the wavenumber range between 2100 and 1900 cm -1 to address this problem.


Structure Input
For creating a structure with the JME Molecular Editor read the editor instructions on how to operate the program.

Minimum Intensity Option
This option allows to set a minimum for peak intensities. Only normal modes with corresponding IR/Raman intensities above the selected threshold will be displayed.

Bond Order
If this flag is set, multiple bonds are plotted by an equivalent number of bond cylinders. The bonds are positioned below and above the averaged plane constructed from the atoms of the bond and all atoms in alpha-position to these, which typically corresponds nicely to the pi-Orbitals.

Bond Color
This is the color of the bonds. You can force a color split when you select Split Atoms as special color.

Number of Frames
Number of frames per cycle. Usefull settings are between 5 and 25 frames. More frames means smoother movement, but also need more processor power.

Amplitude Factor
This option controls the amplitude of the vibration. Usefull settings are between 0.1 and 0.7.

Cycle Time
The period of one standard vibration cycle in seconds.

Encode Force in Frequency
The frequency depends on the force constants. When the Encode Force in Frequency option is set, vibrations with a high force constant will swing faster to visualize this effect.

Technology and Acknowledgments

The CGI script connected to the form runs on a non-GUI version of a class of progammable (in Tcl/Tk and Extensions) general-purpose chemical structure handling programs of the CACTVS system. Using the powerful scripting language interface of these programs, it is possible to implement nearly every graphical or structure handling application very rapidly.

We thank Peter Ertl from Novartis Crop Protection AG for kindly allowing us to use the JME molecular editor. Novartis

We thank Tim Clark from the University of Erlangen for kindly allowing us to use the VAMP program.

Please contact Frank Oellien or Wolf-D. Ihlenfeldt, if you have any questions or comments.