Visual-RHOMBO

Download Visual-RHOMBO

VisualRHOMBO is a program for EPR spectroscopists. It generates effective g-values and powder EPR spectra for half-integer high-spin systems (S=3/2, 5/2, 7/2, or 9/2) of given rhombicity.

ScreenShot Visual-RHOMBO.doc
VisualRHOMBO.zip

Using Visual-RHOMBO

The core of Visual-RHOMBO is a fast version of the old program RHOMBO [WR Hagen (1992) Adv. Inorg. Chem. 38: 165-222] to calculate effective g-values for half-integer spin systems with rhombicity 0 < E/D < 0.34 (a quick intro to the subject can be found in [WR Hagen (2006) Dalton Trans. 2006: 4415-4434]).

Visual-RHOMBO is a one-screen program; so don’t look for child windows. For basic operation locate the button named “RHOMBICITY” on the top, slightly left of the middle of the screen. You can set this so called ‘spin control’ button by putting your mouse on the up or the down arrow and (repeatedly) left-clicking the mouse. Just left of the RHOMBICITY button you find a panel showing, in (nearly) real time, the effective g-values for the rhombicity value set by you.

The effective g-values are for a spin S=3/2 which is the default setting. If you want a different spin value, go to the leftmost panel and make your choice with the “SPIN” radio button. Also, the effective g-values are calculated for a real g-value equal to 2.00. If you have reasons to believe that your real g-value(s) deviates from the free electron value (e.g., your system is not high-spin FeIII) then go to the rightmost panel “Fine tuning” to adjust the value of g-real. Set the mouse arrow at the value of 2.00, delete, and fill in a new value. Enter by hitting ‘enter’ or by hitting ‘Update Spectrum’.

In addition to the effective g-value numbers, Visual-RHOMBO also gives you an actual spectrum. For a particular RHOMBICITY value set by you, hit the “Update Spectrum” button to get the corresponding powder spectrum. The default experimental parameters are in the lower panel left: frequency (9.4 GHz); and field limits (0-5000 Gauss). These can be changed to correspond with your experimental data (which can be read into the program via the “File” menu in the upper left corner; experimental data are ASCII files that consist of 1024 amplitude numbers).

In the ‘Fine tuning’ panel you can adjust the line width (default: 15 Gauss). Also, you can adjust the number of calculated molecular orientations (step-z times step-xy; also known as ‘steps over the unit sphere’). If the calculated spectrum exhibits ‘computer noise’, then increase the number of steps. If you are impatient and you find the simulation time irritatingly long, then try to reduced the number of steps (until ‘computer noise’ starts to appear). The “blow up” button at the very right is to allow you to look at spectral features with very low intensity.

The most advanced option of Visual-RHOMBO is in the panel just right of the middle labeled “Distribution”. Here, you can set a Gaussian distribution of RHOMBICITY values. Just try the default settings (by hitting the “Distributed spectrum” button and watching the blue vertical bar to fill up) to see that a distributed rhombicity quite drastically changes the appearance of the simulated spectrum. The standard deviation (default: 50) is in promille of the rhombicity. Adjust this value to get a fit to your experimental spectrum.

If you get ‘computer noise’ with the distribution option, you have to increase the “number of steps” through the distribution. Use this number with care: it is computationally expensive to significantly increase this number (i.e. the program can seriously slow down). However, for some spectra this is unavoidable, and you just have to be patient. The output number “amplitude” is to compare simulations with different distributions.

The radio button ‘0/00’ versus ‘abs’ allows you to switch to absolute values of “stand. deviation”. The standard deviation is now in reciprocal centimeter units. This is required for spectra with small rhombitity (i.e. near axial spectra). This option is rarely required.

Citation for Visual-RHOMBO: WR Hagen (2007) Wide zero field interaction distributions in the high-spin EPR of metalloproteins. Mol. Phys. 105: 2031-2039.
Please send your comments to: w.r.hagen@remove-this.tudelft.nl

 

 

Name author: Webmaster-BT-TNW
© 2017 TU Delft

Metamenu