View source for Measurement Science Lab: Introduction

==People Involved==

{| align="centre" 
!!!!!

|-
 | '''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:

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

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

#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.


== Write Up ==

=== The Wiki Format ===
Since everyone is used to using [http://www.wordonwiki.com Microsoft Word], why do we [[talks:rzepa2011|use a  Wiki]] for this course?  Well, the  Wiki format has several advantages.
#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.
#The Wiki allows you to include "zoomable" graphics in the form of  SVG (which Gaussview generates), and access to the  17-million large [http://commons.wikimedia.org/wiki/Main_Page WikiCommons] image library, as well as access to the  Wikipedia InterWiki.
#The [[w::Help:Template|template]] concept allows pre-formated entry. There are lots of powerful [[w:Category:Chemical_element_symbol_templates|chemical templates]] available.
#Autonumbered referencing, and particularly cross-referencing, is actually easier than using  Word.
#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.
#It has automatic date and identity stamps for ALL components. 
#And finally, Wiki is an example of a [http://en.wikipedia.org/wiki/Markdown 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 ===
# In the address box, type something like '''wiki.ch.ic.ac.uk/wiki/index.php?title=MSL:XYZ1234''' 
#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.
#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 [[Title=Mod:inorganic_wiki_page_instructions|introductory tutorial]] is available which complements the information here.
*A [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet cheatsheet] summarises the commands with a  [[It:projects|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.
*[[Image:report12345.jpg|right|thumb|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  H<sub>2</sub>O 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)
**# local to the wiki, as  <nowiki>[[mod:writeup|text of link]]</nowiki>
**# remote, as  <nowiki>[http://www.webelements.com/ text of link]</nowiki>
**# Interwiki, as  <nowiki>[[w:Mauveine|Mauveine]]</nowiki>
**# DOI links are invoked using the  DOI template  <nowiki>{{DOI|..the doi string ..}}</nowiki> or the more modern form   <nowiki>[[doi:..the dpi string..]]</nowiki>
**# Links to an Acrobat file you have previously uploaded to the  Wiki can be invoked using this template: <nowiki>{{Pdf|tables_for_group_theory.pdf|...description of link ...}}</nowiki>
**# There are lots of other [[Special:UncategorizedTemplates|templates]] to make your life easier such as the [[w:Template:Chembox|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  <nowiki>[[image:nameoffile.jpg|right|200px|Caption]] </nowiki>
**We support WikiComons, whereby images from the [http://commons.wikimedia.org/wiki/Main_Page content (of ~10 million files)] from [http://meta.wikimedia.org/wiki/Wikimedia_Commons 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 [http://commons.wikimedia.org/wiki/Main_Page 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
***  <nowiki>[[File:Armstrong Edward centric benzene.jpg|thumb|Armstrong Edward centric benzene]]</nowiki>
*Colour can be added (sparingly) using this  {{fontcolor1|yellow|black|text fontcolor}} template.  (invoked as <nowiki>{{fontcolor1|yellow|black|text fontcolor}}</nowiki> )
*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 [[Mod:writeup#Backing_up_your_report|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 [[Mod:writeup#Fixing_broken__Pages|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 [http://www.lego.com Lego]
* [http://en.wikipedia.org/wiki/Raspberry_Pi Raspberry Pi] with an [http://www.adafruit.com/product/1085 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:

{| class="wikitable"
|-
| '''Lab Manual''' || [https://s3-eu-west-1.amazonaws.com/measurement-science-lab/LabManualMSL.pdf Download] || [http://docs.google.com/viewer?url=https%3A%2F%2Fs3-eu-west-1.amazonaws.com%2Fmeasurement-science-lab%2FLabManualMSL.pdf View]
|-
|'''Raspberry Pi Manual''' || [https://s3-eu-west-1.amazonaws.com/measurement-science-lab/RaspberryPiManual.pdf Download] || [http://docs.google.com/viewer?url=https%3A%2F%2Fs3-eu-west-1.amazonaws.com%2Fmeasurement-science-lab%2FRaspberryPiManual.pdf View] 
|-
| '''iPython Notebook Analysis ''' || [https://s3-eu-west-1.amazonaws.com/measurement-science-lab/DataAnalysisScript.ipynb Download] || [http://nbviewer.ipython.org/github/JackPaget/MSLiPythonNB/blob/master/DataAnalysisScript.ipynb View] 
|-
|'''iPython Notebook Data Acquisition'''|| [https://s3-eu-west-1.amazonaws.com/measurement-science-lab/DataAcquisitionScript.ipynb Download] || [http://nbviewer.ipython.org/github/JackPaget/MSLiPythonNB/blob/master/DataAnalysisScript.ipynb View]
|}


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

== The Brief ==
One of the most commonly used measurement tools in the physical and biological sciences is a UV-Vis spectrometer. They can be used for both quantitative and qualitative analysis of samples, and to follow reactions in real-time recording kinetic data. In this lab course you will build your own spectrometer that must be able to:
#Record the absorbance spectrum for a range of concentrations;
#Record the angular dependence of absorbance (i.e. absorbance spectra)
#Understand and determine measurement errors and limitations
#Use the spectrometer to monitor kinetics.

To build your spectrometer you will be supplied with a photodiode detector, a black out cloth, an LED light source, a multi-meter, a power source, slits, a diffraction grating, a protractor, a Raspberry Pi computer, and lots of LEGO! 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 supply additional parts at your request if you can justify their use.

Any measurement including those performed on your Lego spectrometer will have analytical limitations. To maximize the useful information from you measurements it is important understand both instrumental parameters to minimize errors and to use appropriate statistical methods to treat your data. This lab is designed to give you a better understanding of these aspects of collecting spectral data.

A few important points:

#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.
#The experiment is run in groups of 3 – 4 and it is recommended that tasks be allocated to each member to ensure efficient progress.
#To aid your understanding of some of the material you will need to consult other resources (e.g. demonstrators, textbooks, papers, course notes, the internet etc) and we encourage you to do so.
#Your lab notes and the formal write-up (pseudo lab report) will be in the form of a wiki. It will be important to work on this as you go along.
#Although there are 5 parts to this experiment, if time limited, the focus should be on the quality of the results rather than aiming to complete all components.
#All data analysis should be performed during lab hours. A number of resources including the computer room can be used for this.

==Goals of this Lab==
#Understanding the working     principles of a UV-Vis spectrometer.
#Improve '''data handling''' and '''data processing''' by taking into     account instrumental and sample limitations.
#Improve '''decision making''' especially     when it comes to optimisation.
#Improve '''problem solving''' ability.
#Finally, have some fun when designing and     optimizing the LEGO spectrometers.

== Experimental Objectives and Timetable==

The experiment is divided into four parts:

<ol style="list-style-type: lower roman">
<li><b>Building of a UV-Vis spectrometer</b> using a combination of optical components, computer acquisition hardware, and LEGO!</li>
<li><b>How low can you go?</b> Optimisation of the sensitivity and maximising the signal to noise using the dye Methylene Blue.</li>
<li><b>Recording of a complete UV-Vis Spectrum</b> of Methylene Blue. Results to be compared using a commercial instrument.</li>
<li><b>Following a reaction</b> to explore the kinetics of the reduction of methylene blue to leucomethylene blue.</li>
</ol>

===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:

{| align="center" border="1" class="wikitable"
!  
! 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
|-
|}

== Experimental ==
===Part 1: Designing and building a UV-Vis spectrometer===
All spectrometers have five basic components, a light source, a monochromator or diffraction grating, entrance and exit slits, 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. When in doubt ask a demonstrator – they are there to help problem solve. 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.

{|
[[File:Spectrometer.jpg|thumb|center|300px|A schematic of a spectrometer]]
|}

A schematic of a possible configuration for your spectrometer is shown in Figure 1. Key components are as follows:

#'''White light source:''' LED’s are popular options due to their broad spectral range which typically emit between 400-800 nm.
#'''Lens:''' Used for collimating the light and focussing the light on to the sample. Although the location and distance from the light source should be optimized, a good working range is between 4-7 cm.
#'''Entrance and Exit Slits:''' Minimizes scattering and stray light from reaching the detector. These can be mounted directly before and after the sample holder. Templates for both the entrance and exit slits are given.
#'''Diffraction grating:''' The grating splits the white light into individual wavelengths. See below for more details. The grating should be placed near the exit slit.
#'''Detector:''' The photodiode detector will need to be mounted on either a pivot or swivel arm as the signal response from individual wavelengths will need to be recorded (variation of the angle <math>\theta</math> from the grating normal). Although the position of the detector will need to be optimized to maximize the signal response, a reasonable working distance will be between 5-5 cm. A protractor can also be integrated into the spectrometer to convert angle of the detector arm to wavelength.
#'''Recording:''' The detector records its signal as a voltage and will range between 0 and 5 V. Therefore, the detector output can be recorded on either a multimeter or for improved performance on an analogue to digital converter coupled to the raspberry Pi computer. It is recommended that initially the spectrometer is built and tested using a multimeter. Once optimized simultaneous multimeter and computer acquisition can be used.


====The Beer-Lambert Law====
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:  

<div align="center"><math>A = \varepsilon c l</math></div>

Where <math>A</math> is the absorbance,  <math>\varepsilon</math> is the extinction co-efficient,<math>c</math> is the concentration and <math>l</math> is the path length. A plot of absorbance against concentration will give a straight-line  which can be fit to <math>y=mx</math> where <math>m=\varepsilon l</math>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:

<div align="center"><math>A = -\log_{10}\left|\frac{I}{I_0}\right| = \log_{10}\left|\frac{I_0 - I_B}{I - I_B}\right|</math></div>

The intensity of the light, <math>I</math>, is normalised to the intensity recorded for the solvent (or when the concentration is zero), <math>I_0</math>. The photodiode will produce some voltage even in the dark this is known as the dark count, <math>I_d</math>, 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:  

<div align="center"><math>A =  \log_{10}\left|\frac{V_0 - V_B}{V - V_B}\right|</math></div>

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 [http://www.chemguide.co.uk/inorganic/complexions/colour.html chemistry colour wheel].

====Diffraction Grating====
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, <math>\lambda</math>, based on the angle of the light passing from the grating, <math>\theta</math>, and the periodicity of the diffraction grating, <math>d</math>.

<div align="center"><math>d\sin\theta_m = m\lambda</math></div>

In this case <math>\pm m</math> since the sine function is odd the <math>\pm</math> symbol can be dropped and <math>m=1</math>, so the wavelength that will be transmitted after light has passed through your diffraction grating is <math>\lambda = d\sin\theta</math>. 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<math>o</math> 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 [http://www.ch.ic.ac.uk/tcpt/downloads/Measurement_Science_Lab_Manual.pdf 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. Saturation of the detector occurs at 5V therefore, readings should be below this value. '''Note: the Raspberry Pi must be turned on when recording signals from the photodiode even if only using the multimeter.'''    

===== 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 =====

{|
[[File:Raspberry_Pi_B+_top.jpg|thumb|center|300px|The Raspberry Pi B<sup>+</sup> model]]
|}

Once you are at the stage where you are ready to use a Raspberry Pi please follow these [[Measurement_Science_Lab:_Raspberry_Pi| instructions]] on how to use and setup a Raspberry Pi.

===Part 2:Determining the useful concentration range using Methylene Blue ===
The majority of analytical methods follow the instrument response curve as shown in Figure 2. As part of this exercise such a curve should be generated for Methylene Blue with your spectrometer. 

#A useful starting concentration will be 0.3 mM.
#It will be important to minimize the detection limits and modify the instrument accordingly in order to do this. Therefore, you will want to characterize the LOD, LOQ, and LOL.
#Statistical methods should be used to quantify the detection limits. For example, you will want to make note and approximate measurement errors such as listing systematic and random errors, spread of data, mean, standard deviation, sources of noise, and finally averaging and signal to noise.
#The dynamic range should be defined and fit to a linear model.
#How does your detection limit compare to results obtained on a commercial instrument? Commercial UV-Vis spectrometers are available in the lab to assess this aspect. Ask a demonstrator to show you how to use them.

{|
[[File:detection_plots.jpg|thumb|center|300px|Schematic of an instrument response curve. LOD = limit of detection, LOQ = Limit of quantitative measurement, LOL = Limit of linearity.    ]]
|}

===Part 3: Determine the concentration of the unknown.===
A sample of methylene blue with unknown concentration has been found in the lab. An aliquot of this has been given to you to quantify the concentration. Using the information obtained from Part 2, calculate the concentration.

===Part 4: Obtain Absorbance spectra of Methylene Blue and compare with commercial instrument===
Full Absorbance spectra of methylene blue should be obtained at three concentrations. This will then need to be compared to a commercial UV-Vis spectrometer and the following questions will need to be answered. You might have to optimize your methylene blue concentration and slit size accordingly to take into account the saturation of the detector. 

#How does the signal and noise compare between your spectrometer and a commercial instrument?
#How do the signal intensities compare?
#How can your spectrometer be improved?
#Are there any obvious systematic or random errors?
===Part 5: Kinetics associated with mixing methylene blue with ascorbic acid===

You will study the reduction of methylene blue (MB<sup>+</sup>) by ascorbic acid (A) to its colourless form leucomethylene blue.  More specifically you will investigate the dependence of the rate law on the ascorbic concentration acid.

{|
[[File:leuomethylene.jpg|thumb|center|300px|]]
|}

In all cases you will consider, [MB<sup>+</sup>] to be less than 1% of [A], thus ensuring pseudo first-order conditions. A proposed rate law for this reaction is:

<div align="center"><math>-\frac{\mathrm{d}[A]}{\mathrm{d}t}=k_0[A][MB^+]=k_{\mathrm{exp}}[MB^+]</math></div>

Using your spectrometer you should design an experiment to:

#Find the rate constant <math>k_{\mathrm{exp}}</math> for the reduction of [MB<sup>+</sup>] with [A] = 0.045M. In terms of kinetics explain the order of the reaction and comment on its half-life. Discuss your experimental error (it will be helpful to perform repeat measurements). Not more than 3 concentrations are needed.
#Determine the rate constant, <math>k_0</math>, by varying the concentration of [A] and keeping [MB<sup>+</sup>] constant. A potential useful concentration range for [A] would be between 0.002 to 0.045 M. Hint: what you measure will always be the experimental rate constant, you will therefore need to look into methods on how to obtain <math>k_0</math> from this data set.
#How does the rate constant compare to literature?
#What are the statistical errors in your obtained results?