Measurement Science Lab: Introduction

People Involved

Course Co-ordinator:		Dr. Joshua Edel		joshua.edel@imperial.ac.uk
		Dr. Kristelle Bougot-Robin		k.bougot-robin@imperial.ac.uk
Demonstrators:		Silvia Di-Lecce		silvia.di-lecce12@imperial.ac.uk
		Raquel Fraccari		r.fraccari12@imperial.ac.uk
		Markéta Kubánková		m.kubankova13@imperial.ac.uk
		Ali Magness		alastair.magness12@imperial.ac.uk
		Hugh Sowley		hugh.sowley12@imperial.ac.uk
Technicians:		Simon Bastians		s.bastians@imperial.ac.uk
		DeeJay Kristnah		d.kristnah@imperial.ac.uk
		Simon Turner		s.t.turner@imperial.ac.uk

Safety

The lab course is designed to be an enjoyable experience however as with any lab course safety is the number one priority and there are some simple safety rules:

1. YOU MUST WEAR A LAB COAT AND GOOGLES AT ALL TIMES IN THE LABORATORY.

1. YOU MUST NOT EAT OR DRINK IN THE LABORATORY OR BRING ANY FOOD IN WITH YOU.

1. YOU MUST NOT USE YOUR MOBILE PHONE IN THE LABORATORY.

In addition to these rules you must refresh yourself of all the safety regulations from the Foundation Laboratory Course and complete a risk assessment before carrying out any practical work.

Experimental Objectives and Timetable

The experiment is divided into four parts:

1. Building of a UV-Vis spectrometer using a combination of optical components, computer acquisition hardware, and LEGO!
2. How low can you go? Optimisation of the sensitivity and maximising the signal to noise using the dye Methylene Blue.
3. Recording of a complete UV-Vis Spectrum of Methylene Blue. Results to be compared using a commercial instrument.
4. Following a reaction to explore the kinetics of the reduction of methylene blue to leucomethylene blue.

Proposed Timetable

This lab is designed as a problem solving exercise and will run for 2 weeks. There is only one experiment in this lab that is to build and test a spectrometer based on the information held in this lab manual. The lab is designed to take the full 2 weeks and we recommend that you plan you time carefully a proposed time plan could be:

	Monday	Tuesday	Thursday	Friday
Week 1	Initial Spectrometer Design	Build and Improve Initial Design	Perform Concentration Studies	Optimise Spectrometer
Week 2	Perform concentration studies	Generate Absorbance spectra	Comparison with commercial instrument	Present final design

Write Up

The Wiki Format

Since everyone is used to using Microsoft Word, why do we use a Wiki for this course? Well, the Wiki format has several advantages.

1. A full revision and fully dated history across sessions is kept (Word only keeps this during a session). This is more suited for laboratory work, where you indeed might need to go back to a particular day and experiment to check your notes.
2. The Wiki allows you to include "zoomable" graphics in the form of SVG (which Gaussview generates), and access to the 17-million large WikiCommons image library, as well as access to the Wikipedia InterWiki.
3. The template concept allows pre-formated entry. There are lots of powerful chemical templates available.
4. Autonumbered referencing, and particularly cross-referencing, is actually easier than using Word.
5. You (and the graders) can access your report anywhere online, it is not held on a local hard drive which you may not have immediate access to.
6. It has automatic date and identity stamps for ALL components.
7. And finally, Wiki is an example of a MarkDown language, one designed to facilitate writing using an easy-to-read, easy-to-write plain text format (with the option of converting it to structurally valid XHTML).

Creating a Page

1. In the address box, type something like wiki.ch.ic.ac.uk/wiki/index.php?title=MSL:XYZ1234
2. The characters MSL indicate a report associated with the Measurement Science Lab and XYZ1234 is your secret password for the report. It can be any length, but do not make it too long! It should then tell you there is no text in this page. If not, try another more unique password. You should now click on the edit this page link to start. Use a different address for each module of the course you are submitting.
3. It is a good idea to add a bookmark to this page, so that you can go back to it quickly.

Editing a Wiki

An introductory tutorial is available which complements the information here.

• A cheatsheet summarises the commands with a playpen for playing. You can write your report by simply typing the appropriate text as shown in the cheatsheet, or by using the WikEd buttons in Word-style composition.
• 

  The editing environment
  You will need to create a separate report page on this Wiki for each module of the course. Keep its location private (i.e. do not share the URL with others).
• The WikED toolbar along the top of the page has a number of tools for:
  • adding citation references,
  • superscript and subscripting (the H₂O WikEd symbol will automatically do this for a formula),
  • creating tables
  • adding links (Wiki links are internal, External links do what they say on the tin)
    1. local to the wiki, as [[mod:writeup|text of link]]
    2. remote, as [http://www.webelements.com/ text of link]
    3. Interwiki, as [[w:Mauveine|Mauveine]]
    4. DOI links are invoked using the DOI template {{DOI|..the doi string ..}} or the more modern form [[doi:..the dpi string..]]
    5. Links to an Acrobat file you have previously uploaded to the Wiki can be invoked using this template: {{Pdf|tables_for_group_theory.pdf|...description of link ...}}
    6. There are lots of other templates to make your life easier such as the ChemBox
  • If you need some help, invoke it from the left hand side of this page.
• Upload all graphics files also with unique names (so that they do not conflict with other people's names). If you are asked to replace an image, REFUSE since you are likely to be over-writing someone else's image!
  • Invoke such an uploaded file as [[image:nameoffile.jpg|right|200px|Caption]]
  • We support WikiComons, whereby images from the content (of ~10 million files) from Wikimedia Commons Library can be referenced for your own document. If there is a name conflict, then the local version will be used before the Wiki Commons one.
    • To find a file, go to Commons
    • Find the file you want using the search facility
    • Invoke the top menu, use this file in a Wiki, and copy the string it gives you into your Wiki page
    • [[File:Armstrong Edward centric benzene.jpg|thumb|Armstrong Edward centric benzene]]
• Colour can be added (sparingly) using this text fontcolor template. (invoked as {{fontcolor1|yellow|black|text fontcolor}} )
• Save and preview constantly (this makes a new version, which you can always revert to). It goes without saying that you should not reference this page from any other page, or indeed tell anyone else its name.
• Important: Every 1-2 hours, you might also want to make a backup of your report. This is particularly important when adding Jmol material, since any error in the pasted code can result in XML errors. The current Wiki version does not flag these errors properly, but instead just hangs the page. Whilst you can try to repair the page as described below, it is much safer to also have a backup!
• You should get into the habit of recording results, and appropriate discussion, soon after they are available, in the manner of a laboratory note book.

Assessment

This lab has been designed so that you can improve your measurement and data handling skills whilst at the same time understanding that instruments such as a UV-Vis spectrometer should not be treated as a black box. As such no formal mark will be given but rather the groups will be judged based on spectrometer design, discussions with assessor, and quality of experimental data. The winning teams will receive a departmental certificate and vouchers.

Course Materials

The exact setup for this experiment is left up to you, we have provided some guidelines on this wiki and in the lab manuals, and other downloadable materials.

Equipment

We have provided you with a kit that contains all the components that you might need to build a spectrometer, you can use as much or as little of this equipment as you like. If there is something that you feel would be beneficial we may be able to procure it for you if you can justify using the item.

Your kit contains a:

• selection of Lego
• Raspberry Pi with an Adafruit ADC connected

• black out cloth
• pair of slits
• diffraction grating (period 0.1 mm)
• broadband light source
• photodiode
• multimeter
• protractor
• keyboard, monitor, mouse

Downloads

We have created a range of materials for you to use:

Lab Manual	Download	View
Raspberry Pi Manual	cell	cell
iPython Notebook Analysis	cell
iPython Notebook Data Acquisition	cell	cell

Please supplement the information we have provided with your own research.

The Brief

In this lab course you will build your own spectrometer that must be able to:

1. Record the absorbance spectrum for a range of concentrations;
2. Record the angular dependence of absorbance;
3. Follow a colour change reaction.

To build your spectrometer you will be supplied with a photodiode, a box of Lego, a black out cloth, a light source, a multi-meter, a power source and a Raspberry Pi. You can use as many or as few of these items as you like, you are also welcome to make additions to the kit. In some circumstance we may even be able to order additional parts at your request if you can justify their procurement. This lab course is about problem solving and therefore the lab script is not traditional and does not give you a list of steps to follow. Instead it gives an overview of the key parts of a spectrometer and the main points you need to think about in your design.

Designing a Spectrometer

All spectrometers have four basic components, a light source, a monochromator or diffraction grating, a detector and a device to read the detected signal. Before you begin building your spectrometer it is important that you design your spectrometer to make sure it will fulfil the brief’s requirements. This lab course is designed as a problem solving activity so this manual will not tell you how to build a spectrometer but will give you guidance and advice so that your spectrometer is as effective as possible.

IMAGE OF SPECTROMETER

The Lego is for you to build the structure of your spectrometer the spatial design of your spectrometer is up to you. However, remember that it must be able to record a spectrum as a function of angle. The light source is powered by a battery pack and used to provide a broadband beam, this is a fixed part and your group must decide how to include it in your design. The diffraction grating is supplied as a monochromator and should be placed after the sample but before the photodiode. The photodiode is used to convert a photon count into a voltage that can be recorded to construct a spectrum. The device that you use to record the voltage can be either a multimeter or a Raspberry Pi. We strongly advise that you build and test your device with a multimeter before moving to a Raspberry Pi.

The photospectrometer that you create must be able to approximate the extinction co-efficient for a range of substances. This is a simple process that can be calculated from the gradient of a plot of absorbance against concentration by applying the Beer-Lambert Law:

$A = \varepsilon c l$

Where $A$ is the absorbance, $\varepsilon$ is the extinction co-efficient,$c$ is the concentration and $l$ is the path length. A plot of absorbance against concentration will give a straight-line which can be fit to $y=mx$ where $m=\varepsilon l$can be obtained. The path length is the size of your cuvette and so the extinction co-efficient is readily found. The Beer-Lambert law is not applicable at all concentrations since the absorbance will plateau at some concentration rather than continue to infinity. The absorbance is related to the intensity of light:

$A = -\log_{10}\left|\frac{I}{I_0}\right| = \log_{10}\left|\frac{I_0 - I_B}{I - I_B}\right|$

The intensity of the light, $I$, is normalised to the intensity recorded for the solvent (or when the concentration is zero), $I_0$. The photodiode will produce some voltage even in the dark this is known as the dark count, $I_d$, and should be subtracted from each reading. The photodiode converts intensity or photon count into a voltage and therefore can be universally replaced with for voltage to give:

$A = \log_{10}\left|\frac{V_0 - V_B}{V - V_B}\right|$

The light source that you are using is a broadband source that emits white light this light is made up of a spectrum. As the light passes through the sample one particular frequency of light will be absorbed as it provides the required energy for an electronic transition. The light absorbed by solutions of a particular colour can be found from the chemistry colour wheel. A solution of one colour absorbs light of the opposite colour on the colour wheel. To make reduce the signal to noise ratio it is better to concentrate only the frequencies that you are interested in, so if you had a violet solution you would want to record the change in the intensity of yellow light for the optimal result. In a spectrometer the component that selects wavelength is known as a monochromator, the monochromator you will be using a diffraction grating as a monochromator. This delivers a particular wavelength, $\lambda$, based on the angle of the light passing from the grating, $\theta$, and the periodicity of the diffraction grating, $d$.

$d\sin\theta_m = m\lambda$

In this case $\pm m$ since the sine function is odd the $\pm$ symbol can be dropped and $m=1$, so the wavelength that will be transmitted after light has passed through your diffraction grating is $\lambda = d\sin\theta$. So if we had a diffraction grating with a period of 1000 nm and were interested in a violet solution we would want our photodiode to be at an angle of 35$o$ relative to the sample so that it would be detecting the change in yellow light ( 570-590 nm). You must look at the colour of the solution you are testing then position your diode at the optimal angle. This means that your diode must be fixed to a moving arm that is capable of sweeping across a range of angles something that is also vital for task 2. Using this information you should design a spectrometer, remember that science is an iterative process, so you should design, build, test and improve your spectrometer to achieve the optimal results.

Recording Voltage

To turn your spectrometer into a useful device you must connect the photodiode to something that is able to record voltage. In the first instance you should use a multimeter and record the voltage from your photodiode and then analyse the data to produce plots and fits. An iPython Notebook for this course is available from the wiki, however you are free to use any program you like. After you have completed your tests think about how to improve your spectrometer. Once you have a design that you are happy with and that satisfies the brief then you can upgrade your multimeter to a Raspberry Pi and use this to record your voltage and analyse the data on the fly.

Using a Multimeter

Connect the red input to the red diode output and black input to the black diode output. Make sure the multi-meter is set to mV and then record the voltages on the screen in your lab book.

Using a Raspberry Pi

Once you are at the stage where you are ready to use a Raspberry Pi please follow these instructions on how to use and setup a Raspberry Pi.