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Home > News & Events > OceanView Spectroscopy Software and Chemical Kinetics

OceanView Spectroscopy Software and Chemical Kinetics

OceanView is the flagship software program for use with Ocean Optics spectrometers. Beyond simple data visualization, OceanView allows you to generate, customize and save spectroscopy projects using its Schematic View function. Saved projects can then be reloaded or shared with others. The Schematic View presents the data processing steps in a diagram format with icons representing the different devices and processing steps in your project. In the Schematic, you can view and manipulate the flow of data from your spectrometer through each of your processing steps. Data flow is represented by the use of arrows that connect different nodes. The nodes represent points where data is processed or manipulated.

In this project, we monitor the kinetics for a simulated biological reaction by calculating the change in substrate concentration and reaction rate as a function of substrate concentration and stirring speed. In this example, we used red food coloring dye and household bleach to simulate our biological reaction.

OceanView Schematic View as a Teaching Tool

The Schematic View provides you with all of the functionality of the OceanView graph view, plus additional capabilities to customize your spectroscopy measurements:

  • More than 70 algorithm nodes enabling a range of math functions for basic to advanced calculations
  • Subrange node to specify a subset of the spectrum or a single wavelength
  • Interpolation of spectral data to output data at consistent, evenly space intervals
  • Scalar view for monitoring a single value such as TEC temperature or an integral or average over a specified wavelength range
  • Ability to preview spectra in graphs at every step in your process
  • Ability to output the results to visual graphs and Excel-ready CSV files

Although Schematic View may seem daunting at first glance, its value in explaining spectroscopy methods makes it accessible in a way students can appreciate. For example, Schematic View provides a detailed picture of the steps and calculations required to work in a processed mode like Absorbance. Students can explore the spectral data acquired at each step along with the calculations required to turn a raw intensity spectrum into meaningful data.

By visualizing all the processing steps of the experiment in the Schematic View, students have an opportunity to develop a deeper understanding of the measurement technique and to customize data processing for their specific application.

Project Description

This project was created to monitor reaction kinetics (substrate concentration and reaction rate) with changing reaction conditions.

Background

From enzyme reactions within our cells to photosynthesis in leaves, chemical reactions play a vital role in every aspect of our lives. These chemical reactions are dynamic processes that vary with changing conditions. Factors like concentration, temperature, pressure and the presence of a catalyst affect the speed of a reaction. The study of chemical kinetics is used to characterize these processes and improve our understanding of how these factors and others change the outcome of a chemical reaction.

In this project, we used red food coloring and household bleach to simulate a biological reaction. As each sample is added to the reaction vessel, the reaction rate and substrate concentration change as the reaction occurs.

Schematic

QE Pro Kinetics Demo Schematic

Project

QE Pro Kinetics Demo Screen Capture

Project Import Procedure

Import the project into OceanView by going to File| Share project| Import. OceanView will guide you through the steps necessary to swap the spectrometer you are using into the project including measuring a new reference and background spectrum.

This project was created to measure changes in the absorbance of red food coloring dye in bleach in the Vis-NIR wavelength range. Changes in substrate concentration and reaction rate are calculated from the absorbance at 522 nm (absorbance maximum for red food dye). If you are using a sample other than red food dye, you will need to make a few changes to the values specified in various nodes in the Schematic.

First, update the wavelength for the absorbance maximum specified in each of the 522 nm nodes to match the absorbance maximum for your sample. Change this value by double clicking the node to open it. This absorbance maximum value must match the absorbance maximum for your sample, as it is used to show the trend in absorbance over time, to calculate the rate constant and to calculate substrate concentration.

Also, you will need to update the values in the Extinction 1 and Rate Constant nodes to match the previously calculated or literature reported extinction coefficient and rate constants for your sample and reaction. Finally, if you are using a sample cell with a pathlength other than 1 cm, you will need to update the value in the Path Length 1 node as well.

The Onboard Buffer acquisition in the lower part of the Schematic is used to monitor and display the number of spectra buffered on board the QE Pro spectrometer in real time. The QE Pro has an onboard buffer that can hold up to 15,000 spectra. This buffer ensures that you will not miss a single data point during your kinetics measurements. This level of data integrity is absolutely critical for kinetics and other time based measurements where every single data point counts.

Summary

Chemical kinetics is a staple in many undergraduate teaching laboratories. In this case, the reaction involved the oxidation of red food coloring dye by bleach. As the dye reacts with the bleach, the color and visible absorbance spectrum disappears. These visual changes help to underscore what the students observe in the spectra.

Additional Information