Tutorial: Kinetics of Visible Spectra in one JCAMP-DX file: the Aquation of trans-[Co(en)₂Cl₂]⁺

Introduction

• JCAMP-DX is an internationally accepted format that is suitable for spectra collected from a wide range of methods, spectroscopy, and instrumentation. A single JCAMP-DX spectrum can store a series of spectra using multi BLOCKS
• Here is a simple example of obtaining the kinetics of aquation of trans-[Co(en) ₂Cl₂]⁺ from a single JCAMP-DX file, which includes a series absorbance (Vis) spectra using 5 data blocks.
• More examples of JCAMP-DX data can be found at http://wwwchem.uwimona.edu.jm:1104/spectra/testdata/index.html

• Basic information on the experiments can be found in the header of the downloaded blckpac1.jdx file:

  ##TITLE= Aquation of trans-[Co(en)2Cl2]+
  ##DATA TYPE= LINK
  ##BLOCKS= 5
  ##ORIGIN= Dept of Chem, UWI, Mona, JAMAICA
  ##OWNER= public domain
  ##TITLE= (t1) Aquation of trans-[Co(en)2Cl2]+
  ##JCAMP-DX= 4.24
  ##DATA TYPE= UV/VIS SPECTRUM
  ##BLOCK_ID=1
  ##ORIGIN= Dept of Chem, UWI, Mona, JAMAICA $$Exported PE UV WinLab Data File
  ##OWNER= public domain
  ##DATE= 96/11/04
  ##TIME= 18:07:10.00
  ##SPECTROMETER/DATA SYSTEM= PERKIN-ELMER LAMBDA 19 UV/VIS/NIR UV
  

• The Vis spectra series are displayed here with their time stamps:
  

Steps

1. Prepare xaxisfile by extracting time information from all blocks (Optional)

• The time courses of the aquation of trans-[Co(en)₂Cl₂]⁺ was recoreded in this example. This time at which each spectrum(block) was collected is given
  by the ##TIME field, for example:

  ##TIME= 18:07:10.00
  

• Although TREND does not need the temporal information to perform PCA analysis on this kinetic experiment, it will be needed to plot the time-course of the reaction with its time scale.

• Since the x axis points in xaxisfile must be integer or floating point numbers, these need to be extracted from the JCAMP-DX (.jdx or .dx) file.

• 1.1. Extract time information
  I. This can be done manually or running the following command in a Linux or macOS terminal using this syntax:

  cat blckpac1.jdx |grep "TIME"|awk '{print $2}' > time.txt
  

  II. Then the time.txt contains the following lines:

  18:07:10.00
  18:07:33.00
  18:08:07.00
  18:08:40.00
  18:09:14.00
  

• 1.2. Convert time.txt to xaxisfile
  I. Open time.txt using Excel or OpenOffice
  II. Convert time to seconds in Excel
  The time format in the A column is hh:mm:ss.ff, the simplest way is to convert time to units of seconds in column B, using the formula depicted. This may require first setting the format of the cells of column B to "general".
  
  III. Calculate time change as difference between each time point to the first time point
  IV. Now save the column C to a file x-axis.txt, which will be used as xaxisfile for trendmain or trendplot

  0.00
  23.00
  57.00
  90.00
  124.00
  

2. Do PCA on the multi-block JCAMP-DX file

2.1 First launch trendmaingui, and specify options as illustrated in the menu:

2.2 Press the Start button, TREND will run quickly, resulting in text appearing in the window as shown:

The corresponding command is:

trendmain.exe -f blckpac1.jdx -t jcamp -s noscaling  -x x-axis.txt -u second -o Aquation --report

2.3 After trendmain finishes, a report in HTML format appears, and in this example is named Aquation-report.html. Its scree plot (a bar chart) indicates that there is only principal component.

Note that TREND does not currently support reconstruction of JCAMP-DX files.