Ultraviolet spectra
Introduction
Ultraviolet-visible spectroscopy (UV-vis) is a spectroscopic technique dealing with the visible and ultraviolet region of the electromagnetic spectrum (wavelengths between 100 and 700 nm). It measures the amount of light absorbed by or transmitted through a sample compared to a reference sample (blank). It is widely used in analytical chemistry for quantitative determination of different analytes. The UV-vis spectrum can be visualized in a graph of absorbance of light with respect to the wavelength (nm). UV-vis spectroscopy exploits the change of electronic states of a molecule due to light absorption at a specific frequency, characteristic to its structure.
Analyze
Upload and visualize spectra
In this view there are different ways to upload a UV spectrum in either a JCAMP or a text file format.
How to upload a file
In this view, it is possible to upload one or more spectra of a target sample by drag/drop either a JCAMP-DX or a text file. An individual spectrum can be visualized and analyzed by clicking on its name in the "List of files". Several spectra can also be compared. The information about the chosen sample can be found in the colored window on the right.
Upload spectrum
You can upload a spectrum in 3 different ways:
- by dragging your files and then dropping them in the designated zone.
- by clicking on the upload zone and selecting the files to upload.
- by copying the spectrum into the clipboard and then pasting it using CTRL+V (or ⌘+V on MacOS).
The format of the file to be uploaded should be JCAMP-DX (extension .dx or .jdx), this is the usual format used on most IR spectrophotometers.
Once the spectrum is uploaded you can visualize it by clicking on its name and manipulate it.
How to manipulate a spectrum.
Manipulating the spectrum
Once uploaded, you can select the spectrum on the right in the List of files tab. Once selected the spectrum will appear in the Analyse spectrum tab.
You can manipulate the graph in the following ways:
- SHIFT + drag on the graph to translate it
- Click + drag to zoom in on the selected window
- Double click to return to default view
- Scroll the mouse wheel to rescale the y-axis of the spectrum
- SHIFT + double click to zoom out progressively
Don't forget to Save data before leaving the page!
Peak picking
It is possible to manually pick peaks on an ultraviolet spectrum by holding down the ALT key, and then left-clicking on the peaks of interest.
Informations about the manual peak picking.
Peak picking
It is possible to manually pick peaks in a spectrum by holding down the ALT key, and then left-clicking on the peaks of interest.
The application will systematically look for the strongest signal close to the wavelength that has been clicked. The peaks will be stored in a separate tab.
The algorithm automatically classifies the peaks.
The application will systematically look for the strongest signal close to the wavelength that has been clicked.
The peaks will be displayed in the UV peaks
tab. The signal strength is given automatically. The categorization S, m and w for strong, medium and weak, is based on the highest and lowest selected peak. All peak wavelenghts and absorbance are reported in a compact format ready for publication.
You can edit the peak kind by double clicking on the kind in the peak table. The compact format of the peak list will automatically update.
Alternatively, the system allows to perform peak picking automatically within a certain range and signal-to-noise ratio.
Informations about the auto peak picking.
Auto peak picking
The system can automatically pick peaks of interest for a specific range of wavenumbers with a defined noise level using Auto peak picking tab.
Auto peak picking is based on the Savitzky Golay filter.
You can remove a specific signal using the 
icon or all the signals at the time using the 
icon.
Compare
You can compare multiple UV spectra by first opening up a spectrum, and then clicking Compare on top of the UV spectrum.
After which, under List of selected entries, you can choose the other molecule which has the spectrum that you would like to compare. You can then add all the spectra attached to the molecule using the 
icon by double clicking on the sample or display only one of the spectra by first clicking on the sample, then clicking on the specific spectrum in List of UV spectra. You can also use the and icons to manage the view (check animation below).
The spectra will then be both displayed on top of each other. You can also freely hide selected graphs and change the color by clicking the color bar.
How to show/hide spectra.
Visualising spectra
If you wish to see only certain spectra, it is possible to selectively hide (or delete) them.
In order to do so, use the 
buttons on the top panel of the displayed spectra list.
You can also change the color of an individual spectrum in the displayed spectra tab with a double click.
In many tables it is possible to select which columns to display. This is achieved by clicking on the icon.
After clicking on the icon a dialog box opens that allows to add a new column.
There are 5 parameters to fill for a new column:
- name: the column name. This will be displayed as the header to the column.
- rendererOptions: options that allows among other to format numbers. One very useful formatter is
numeral(see after) - width: number of pixels for the specific column. May stay empty for automatic layout.
- forceType: select how to display complex values (see later)
- jpath: where to find the information to display in the column
In order to add a new column you need to select the jpath using the hierarchical drop down menu.
Columns can be moved or rearranged as well.
rendererOptions: numeral
number,
| Value to format | rendererOptions | Result |
|---|---|---|
| 12.345678 | numeral:'#.##' | 12.34 |
| 12.3 | numeral:'#.00' | 12.30 |
| 0.3 | numeral:'#.0 %' | 30.0 % |
forceType
In the database some values are stored as an object that needs to be displayed to the user in an intuitive way.
For example the unit type will store in the database the value using as units SI (we convert the data to the units defined by the 'standard international') and specify in which units the user would like to display the data. So in the following example we are in fact storing the value -150°C by storing the value in SI (Kelvin) and specifying that the user wants to see it in °C.
{
"SI": 123.15,
"unit": "°C"
}
Another example is the valueUnits type that will store the data in 2 different properties
(value and unit). In this case the value is stored in the specified units and there is no conversions.
{
"value": 123,
"units": "°C"
}
While this way to store the data in the database is very practical it is not the way that the user would like to see his results. We have therefore the possibility to forceType: define how the user would like to see the results.
Other types include mf. This formatter allows to correctly display a molecular formula that is stored in the database as "C10H20O3". i.e. it will put the numbers in subscript (C₁₀H₂₀O₃).