I was recently tasked with an interesting challenge by a client and it had me exercising spectral interpretation muscles I have not used in a long time. They sent me a dozen unknown mixture spectra to analyze prior to my teaching an on-site course on the topic at their facility (for the advantages of on-site FTIR training, including free customization, click here http://www.spectros1.com/course_custom.html ). These spectra are perhaps the most difficult to interpret because they are unknowns and because in mixture spectra it can be difficult to figure out what functional groups give rise to what peaks. As I was wading through these spectra I became conscious of the process I was following, and since I had some success I thought I would share that process with my readers.
In my Infrared Spectral Interpretation I course (outline here: http://www.spectros1.com/c-spectral-i.html ) I teach attendees a 12-step program for successfully interpreting spectra. I followed the 12 steps for each spectrum, but in several cases I got to the end of the process without having made much progress. This is when Step 12, "Get Help", comes into play. I found the first thing I did after completing my analysis of a difficult unknown mixture spectrum was to do a library search. In one case the search was of high quality and allowed me to identify the main component in an unknown.
In a few other cases the library search was inconclusive. This is when I hit the literature. I have published a book on Infrared Spectral Interpretation (more info here: http://www.spectros1.com/books.html) and I also have on my bookshelf a number of IR spectral interpretation books by other authors, some of which are more far ranging than my introductory text. Between these books I was able to narrow down some of the unknowns to categories of molecules. For instance, that several of the samples contained carboxylates.
After this I looked up reference spectra of possibilities in a specific chemical class in an infrared spectral atlas. Such an atlas is a collection of infrared spectra organized by functional group. My favorite infrared spectral atlas is the comprehensive 3-volume collection published by Aldrich Chemical (more info here: http://www.sigmaaldrich.com/catalog/ProductDetail.do?N4=Z286001ALDRICH&N5=SEARCH_CONCAT_PNOBRAND_KEY&F=SPEC). This compendium contains over 18,500 spectra organized into 53 functional groups. The beauty of this atlas is that you can look at many spectra of the same type of molecule together and quickly learn the pattern of peaks that is diagnostic for that functional group. I did this with a few of the unknowns to become more familiar with the spectra of functional groups that the library search suggested were present in a sample. If I wanted to look up a specific reference spectrum the Aldrich Spectral Atlas could be used for that. However, Aldrich also sells the Aldrich Spectral Viewer (details here: http://www.sigmaaldrich.com/labware/learning-center/spectral-viewer.html). This is an electronic collection of 11,000 infrared spectra that can be searched by compound name or functional group. I find that if I have to look up the spectrum of a specific compound the Spectral Viewer is faster than the Spectral Atlas. The spectral viewer is nice because the spectra are in color, the display limits can be altered, and peaks can be picked and marked. By looking up spectra of functional groups I made progress, and in a few cases by looking up specific spectra I was able to identify specific compounds in a mixture. In the end, I was able to identify specific molecules in a number of the unknowns. However, in a few cases I was only able to suggest what functional groups might be present in a sample.
So, the key then to analyzing unknown mixture spectra is to execute the first 11 steps of the 12-Step interpretation strategy I have discovered. Then exercise the "Get Help" step by using library searches, spectral atlases, and the spectroscopy literature. Using these techniques unknown mixture spectra can be convinced to yield some of their secrets.
Monday, April 20, 2009
Monday, April 13, 2009
Where CSI Gets it Wrong
Where CSI Gets it Wrong
I recently had the privilege of teaching my FTIR Analysis of Controlled Substances course at a well known forensics lab; one of the ones they make TV shows about (course outline is here: http://www.spectros1.com/c-forensic.html). The simple act of writing the letters "CSI" on the board elicited a chorus of groans and laughter from the roomful of forensic scientists taking the course. For those of you who don't watch much TV, the letters "CSI" stand for "Crime Scene Investigation", a series of shows about how forensic scientists help solve crimes. The chorus of groans and laughter is based on the fact that the science on these shows is so inaccurate as to be laughable.
The first thing CSI gets wrong is the role of forensic scientists in crime fighting. They portray lab workers donning bullet proof vests, carrying guns, and chasing down and arresting bad guys. Now in some states forensic scientists may go to the occasional crime scene, but there are no forensic lab workers that I am aware of that carry a gun and arrest people. In many forensics labs there is a strict division of labor between the police, who arrest the bad guys and collect evidence at crime scenes, and the civilian scientists who analyze crime scene evidence and testify about it in court.
Another thing CSI gets wrong is the speed of the analyses performed in a forensics lab. In the world of CSI it apparently only takes a few minutes to run a DNA analysis and identify the bad guy. In the real world it usually takes days or weeks to get DNA results back, and although DNA is a powerful forensics tool it may not be definitive because you can not identify someone who is not in your DNA database.
It is true of CSI, and most movies and TV shows, that the actors and actresses are exceedingly good looking. Now, I have great respect and admiration for the professionalism of forensic scientists and the important role they play in promoting public safety. However, I can tell you that they all don't look like supermodels :-).
But what CSI really gets wrong is the way it portrays the use of FTIR in forensic labs. If you watch the show closely you may have noticed there is a Thermo Nicolet FTIR on the set of one of the CSI shows. Several years ago a Nicolet salesman told me the story of how this came to be. The producers of the show approached Nicolet and asked them for a free FTIR in return for the free publicity Nicolet would enjoy by having the instrument appear on TV. The folks at Nicolet were a little leery of handing over an instrument worth tens of thousands of dollars for free. They had the intelligence to ask the producers of CSI, "Will you ever use the FTIR to perform an analysis?". The answer was no. So, instead of giving the show a complete instrument Nicolet proposed giving them the plastic shell that covers the instrument but with nothing inside of it. This was acceptable to the producers, and that is how a Nicolet "FTIR" came to be featured on a TV show.
Several years ago an episode of CSI featured the use of the FTIR in one of their shows, and they got it terribly wrong. On TV they showed a red visible light laser, apparently a He-Ne laser, as the light source of the FTIR As I teach in my Fundamentals of FTIR course all FTIRs contain a visible light laser that is used to measure the optical path difference of the interferometer. However, this laser is NOT the infrared source because you can't measure an infrared spectrum with visible light. Also, because a laser gives off only one wavelength of light it is impossible to use it to measure a spectrum, which requires many wavelengths of light. Another thing I teach in my Fundamentals of FTIR course is that FTIR is a form of molecular spectroscopy. Individual atoms are not chemically bonded to anything, do not possess vibrations, and hence generally don't have a mid-infrared spectrum. This makes FTIR inappropriate for elemental analysis. On the same show mentioned above they were using the FTIR to perform an atomic analysis on a sample. This is more than I could take, and I have not watched an episode of the show since.
These scientific inaccuracies may seem amusing, but they can have a negative effect upon the public safety of our country. A number of forensic scientists and police officers that I have talked to have said there exists a "CSI effect". Potential jurors, defense attorneys, and even some prosecutors have been so swept up into the imaginary world of the TV show that they have totally unrealistic expectations of what a crime lab can do. Prosecutors expect DNA test results back in hours and get cranky when they do not get what they want. But the scariest story I heard involved a juror. This person had watched so much CSI that he fancied himself an expert in the field. When the police did not run the tests that this juror thought they should have run, he assumed the police were hiding something and as a result voted to acquit a person who may very well have been guilty. So, as entertaining as these shows may be, there is always a cost to portraying things that are not true.
I recently had the privilege of teaching my FTIR Analysis of Controlled Substances course at a well known forensics lab; one of the ones they make TV shows about (course outline is here: http://www.spectros1.com/c-forensic.html). The simple act of writing the letters "CSI" on the board elicited a chorus of groans and laughter from the roomful of forensic scientists taking the course. For those of you who don't watch much TV, the letters "CSI" stand for "Crime Scene Investigation", a series of shows about how forensic scientists help solve crimes. The chorus of groans and laughter is based on the fact that the science on these shows is so inaccurate as to be laughable.
The first thing CSI gets wrong is the role of forensic scientists in crime fighting. They portray lab workers donning bullet proof vests, carrying guns, and chasing down and arresting bad guys. Now in some states forensic scientists may go to the occasional crime scene, but there are no forensic lab workers that I am aware of that carry a gun and arrest people. In many forensics labs there is a strict division of labor between the police, who arrest the bad guys and collect evidence at crime scenes, and the civilian scientists who analyze crime scene evidence and testify about it in court.
Another thing CSI gets wrong is the speed of the analyses performed in a forensics lab. In the world of CSI it apparently only takes a few minutes to run a DNA analysis and identify the bad guy. In the real world it usually takes days or weeks to get DNA results back, and although DNA is a powerful forensics tool it may not be definitive because you can not identify someone who is not in your DNA database.
It is true of CSI, and most movies and TV shows, that the actors and actresses are exceedingly good looking. Now, I have great respect and admiration for the professionalism of forensic scientists and the important role they play in promoting public safety. However, I can tell you that they all don't look like supermodels :-).
But what CSI really gets wrong is the way it portrays the use of FTIR in forensic labs. If you watch the show closely you may have noticed there is a Thermo Nicolet FTIR on the set of one of the CSI shows. Several years ago a Nicolet salesman told me the story of how this came to be. The producers of the show approached Nicolet and asked them for a free FTIR in return for the free publicity Nicolet would enjoy by having the instrument appear on TV. The folks at Nicolet were a little leery of handing over an instrument worth tens of thousands of dollars for free. They had the intelligence to ask the producers of CSI, "Will you ever use the FTIR to perform an analysis?". The answer was no. So, instead of giving the show a complete instrument Nicolet proposed giving them the plastic shell that covers the instrument but with nothing inside of it. This was acceptable to the producers, and that is how a Nicolet "FTIR" came to be featured on a TV show.
Several years ago an episode of CSI featured the use of the FTIR in one of their shows, and they got it terribly wrong. On TV they showed a red visible light laser, apparently a He-Ne laser, as the light source of the FTIR As I teach in my Fundamentals of FTIR course all FTIRs contain a visible light laser that is used to measure the optical path difference of the interferometer. However, this laser is NOT the infrared source because you can't measure an infrared spectrum with visible light. Also, because a laser gives off only one wavelength of light it is impossible to use it to measure a spectrum, which requires many wavelengths of light. Another thing I teach in my Fundamentals of FTIR course is that FTIR is a form of molecular spectroscopy. Individual atoms are not chemically bonded to anything, do not possess vibrations, and hence generally don't have a mid-infrared spectrum. This makes FTIR inappropriate for elemental analysis. On the same show mentioned above they were using the FTIR to perform an atomic analysis on a sample. This is more than I could take, and I have not watched an episode of the show since.
These scientific inaccuracies may seem amusing, but they can have a negative effect upon the public safety of our country. A number of forensic scientists and police officers that I have talked to have said there exists a "CSI effect". Potential jurors, defense attorneys, and even some prosecutors have been so swept up into the imaginary world of the TV show that they have totally unrealistic expectations of what a crime lab can do. Prosecutors expect DNA test results back in hours and get cranky when they do not get what they want. But the scariest story I heard involved a juror. This person had watched so much CSI that he fancied himself an expert in the field. When the police did not run the tests that this juror thought they should have run, he assumed the police were hiding something and as a result voted to acquit a person who may very well have been guilty. So, as entertaining as these shows may be, there is always a cost to portraying things that are not true.
Sunday, March 29, 2009
Pittcon Follow-Up:Portable Hand Held FTIRs Really Exist!
Pittcon Follow-Up: Portable Hand Held FTIRs Really Exist!
In my last post I was bemoaning the head cold I had while trying to navigate the grand halls of Pittcon. The head cold turned into a sinus infection, but thanks to the modern miracle of antibiotics I am now back in writing form.
One of the neatest things I saw at the Pittsburgh Conference in Chicago (it really sounds like the meeting planners don't know their geography) were hand held FTIRs. These are portable FTIR systems that are light enough to be held in one hand, are battery powered, and have enough on-board computing power to allow you to take spectra, identify unknowns, perform quantitative analyses, and diagnose instrument problems. These systems are a true miracle to me. I am old enough to have worked with some of the first commercial FTIR systems built in the 1970s. These were huge machines that weighed hundreds of pounds, were very sensitive to vibration, and were complex to run. Today we have FTIR systems that are rugged enough to be taken out into the field, weigh only several pounds, and can be operated by anyone with a little bit of training. I will review one instrument here, and another in a few days.
The first system I saw at Pittcon is made by Ahura Scientific of Wilmington, MA. It is called the TruDefender FT, although that moniker sounds like it could also be applied to a super hero. The system is 7.8" x 4.4" x 2.1 and weighs under 3 pounds. It uses a diamond ATR sensing head and can run on batteries for more than two hours. The spectrometer scans from 4000 to 650 cm-1, which indicates to me it probably has a ZnSe beamsplitter, and is capable of 4 cm-1 resolution. The unit seems to be designed for hazardous materials and homeland security applications. The area around a hazardous waste spill or bio-terrorism event is called the "hot zone". Ahura says their instrument is small enough and rugged enough to be taken right into the hot zone to examine the suspect material in-situ. There is no need to carry the material out of the hot zone to the instrument risking further contamination and wasting precious time.
Ahura Scientific claims their software can identify compounds from their infrared spectrum and provides, " definitive results that don’t require user interpretation or judgment" (this quote is from their website). I approached the people at the Ahura booth at Pittcon to ask them to explain how their identification software system works. They said "it's a trade secret" which I did not find helpful. More information on the TruDefender FT can be found here
http://www.ahurascientific.com/chemical-explosives-id/products/trudefenderft/index.php# .
In my last post I was bemoaning the head cold I had while trying to navigate the grand halls of Pittcon. The head cold turned into a sinus infection, but thanks to the modern miracle of antibiotics I am now back in writing form.
One of the neatest things I saw at the Pittsburgh Conference in Chicago (it really sounds like the meeting planners don't know their geography) were hand held FTIRs. These are portable FTIR systems that are light enough to be held in one hand, are battery powered, and have enough on-board computing power to allow you to take spectra, identify unknowns, perform quantitative analyses, and diagnose instrument problems. These systems are a true miracle to me. I am old enough to have worked with some of the first commercial FTIR systems built in the 1970s. These were huge machines that weighed hundreds of pounds, were very sensitive to vibration, and were complex to run. Today we have FTIR systems that are rugged enough to be taken out into the field, weigh only several pounds, and can be operated by anyone with a little bit of training. I will review one instrument here, and another in a few days.
The first system I saw at Pittcon is made by Ahura Scientific of Wilmington, MA. It is called the TruDefender FT, although that moniker sounds like it could also be applied to a super hero. The system is 7.8" x 4.4" x 2.1 and weighs under 3 pounds. It uses a diamond ATR sensing head and can run on batteries for more than two hours. The spectrometer scans from 4000 to 650 cm-1, which indicates to me it probably has a ZnSe beamsplitter, and is capable of 4 cm-1 resolution. The unit seems to be designed for hazardous materials and homeland security applications. The area around a hazardous waste spill or bio-terrorism event is called the "hot zone". Ahura says their instrument is small enough and rugged enough to be taken right into the hot zone to examine the suspect material in-situ. There is no need to carry the material out of the hot zone to the instrument risking further contamination and wasting precious time.
Ahura Scientific claims their software can identify compounds from their infrared spectrum and provides, " definitive results that don’t require user interpretation or judgment" (this quote is from their website). I approached the people at the Ahura booth at Pittcon to ask them to explain how their identification software system works. They said "it's a trade secret" which I did not find helpful. More information on the TruDefender FT can be found here
http://www.ahurascientific.com/chemical-explosives-id/products/trudefenderft/index.php# .
Tuesday, March 10, 2009
Pittcon 2009 Day 1: FTIR Mixture Analysis Software Packages
The first day of Pittcon was exciting for me, for the wrong reasons. I have come down with a nasty cold which has made standing and talking, the most common activity at Pittcon, a little more interesting than I would like. I hope I have not inadvertently infected any of my colleagues.
I visited a number of FTIR instrument company booths on Monday. There is much new and interesting to talk about, but one thing that really excites me are new software programs that assist the FTIR user in mixture analysis. As I mention in my Fundamentals of FTIR and IR Spectral Interpretation I courses, mixture analysis is the biggest practical disadvantage of FTIR. The problem is that the more chemically complex a mixture becomes the more complex the infrared spectrum becomes, making it harder to figure out what peaks are from what molecules. In my training courses I teach attendees the 4 ways of tackling mixtures. These mixture analysis software packages may represent a fifth way.
Time for a disclaimer. Two vendors, the Bio-Rad Informatics division and Thermo-Nicolet are demonstrating mixture analysis software here at Pittcon. My discussion of their offerings is in no way an endorsement of their products. If I find other companies showing mixture analysis software I will talk about them in a later post.
These mixture analysis software packages work like library searching, which is a technique many FTIR users are familiar with. In this case the mixture spectrum is selected, one or more spectral libraries are selected, and then the mixture search is performed. The algorithms on both systems are trade secret, but my hunch is that they use some sort of chemometric modeling, perhaps principle components or partial least squares analysis. For the results to work out well you have to tell the software how many different chemical components you think there are in the sample. Knowing this information greatly improves the quality of the results. However, as those of us who work in the real world know, we don't always know the exact number of components in a sample. I also noticed that for the most part you are limited to mixtures with 2, 3, or 4 components. Not surprisingly, the calculation time increases for each added component.
My hunch then is if you tell the software you have a two component mixture it will take spectra from the selected libraries two at a time, calculate mixture spectra from them, and compare them to your sample spectrum. This comparison gives a number similar to the hit quality index (HQI) in a normal library search. The pair of library spectra that when added together give the best match to your sample spectrum should give the best HQI. You can visually compare the calculated and sample spectra. Other tools, including the spectral residual, which is the result of subtracting the calculated spectrum from the sample spectrum, are available to judge the quality of the results. I think certain FTIR users, particularly those unfamiliar with IR Spectral Interpretation, may find this type of software package useful.
I am sure many of you are wondering whether these mixture analysis programs can provide quantitative information i.e.the percentage of different compounds in a sample. There was much careful talk about this issue from which I was not able to draw a conclusion. This is something I would like to see an unbiased third party put to the test (hint hint).
A blurb about the Bio-Rad software is here: http://collateral.knowitall.com/collateral/95372-Mixture_Analysis_Datasheet.pdf#zoom=75%
A blurb about the Nicolet software is here: http://www.thermo.com/com/cda/product/detail/1,,10137344,00.html
I visited a number of FTIR instrument company booths on Monday. There is much new and interesting to talk about, but one thing that really excites me are new software programs that assist the FTIR user in mixture analysis. As I mention in my Fundamentals of FTIR and IR Spectral Interpretation I courses, mixture analysis is the biggest practical disadvantage of FTIR. The problem is that the more chemically complex a mixture becomes the more complex the infrared spectrum becomes, making it harder to figure out what peaks are from what molecules. In my training courses I teach attendees the 4 ways of tackling mixtures. These mixture analysis software packages may represent a fifth way.
Time for a disclaimer. Two vendors, the Bio-Rad Informatics division and Thermo-Nicolet are demonstrating mixture analysis software here at Pittcon. My discussion of their offerings is in no way an endorsement of their products. If I find other companies showing mixture analysis software I will talk about them in a later post.
These mixture analysis software packages work like library searching, which is a technique many FTIR users are familiar with. In this case the mixture spectrum is selected, one or more spectral libraries are selected, and then the mixture search is performed. The algorithms on both systems are trade secret, but my hunch is that they use some sort of chemometric modeling, perhaps principle components or partial least squares analysis. For the results to work out well you have to tell the software how many different chemical components you think there are in the sample. Knowing this information greatly improves the quality of the results. However, as those of us who work in the real world know, we don't always know the exact number of components in a sample. I also noticed that for the most part you are limited to mixtures with 2, 3, or 4 components. Not surprisingly, the calculation time increases for each added component.
My hunch then is if you tell the software you have a two component mixture it will take spectra from the selected libraries two at a time, calculate mixture spectra from them, and compare them to your sample spectrum. This comparison gives a number similar to the hit quality index (HQI) in a normal library search. The pair of library spectra that when added together give the best match to your sample spectrum should give the best HQI. You can visually compare the calculated and sample spectra. Other tools, including the spectral residual, which is the result of subtracting the calculated spectrum from the sample spectrum, are available to judge the quality of the results. I think certain FTIR users, particularly those unfamiliar with IR Spectral Interpretation, may find this type of software package useful.
I am sure many of you are wondering whether these mixture analysis programs can provide quantitative information i.e.the percentage of different compounds in a sample. There was much careful talk about this issue from which I was not able to draw a conclusion. This is something I would like to see an unbiased third party put to the test (hint hint).
A blurb about the Bio-Rad software is here: http://collateral.knowitall.com/collateral/95372-Mixture_Analysis_Datasheet.pdf#zoom=75%
A blurb about the Nicolet software is here: http://www.thermo.com/com/cda/product/detail/1,,10137344,00.html
Thursday, March 5, 2009
I'm Off to Pittcon
I will be gone from March 9-12 to attend the Pittsburgh Conference on Analytical Chemistry & Applied Spectroscopy, which is being held in Chicago strangely enough. This is the show where FTIR manufacturers trot out their new products. As a service to you, dear reader, I will gather information on the latest and greatest FTIR instrumentation and report it to you here once I return from my trip. So make sure to come back soon.
ATR III: How Wavenumber Impacts DP
The first parameter to consider in the ATR depth of penetration (DP) equation is W, the wavenumber. At first glance the presence of this parameter in the equation should strike you as bizarre. In a transmission sampling experiment the infrared beam passes through a thin film of sample and all wavenumbers of light see the same sample thickness. Since wavenumber appears in the denominator of the DP equation, as W goes up DP goes down. This means, for example, that in an ATR experiment 1000 cm-1 light penetrates further into samples than 3000 cm-1 light does. Since peak size is proportional to pathlength, the relative intensities in ATR spectra are different than in spectra taken via other sampling techniques. In general in ATR spectra the peaks at high wavenumber are smaller than the peaks at low wavenumber.
This point is illustrated in the figure pasted into this blog post which shows the ATR and non-ATR spectra of sucrose (table sugar). Note in the ATR spectrum (top) the peaks at low wavenumber are much bigger than the peaks at high wavenumber, whereas in the non-ATR spectrum (bottom) the peaks at low and high wavenumber are about the same size.
This phenomenon has important implications for how we use ATR spectra. Since ATR spectra look different than non-ATR spectra it is best to only compare ATR spectra to each other. This also means you will get better library searching results by only searching ATR spectra against ATR libraries. If you own an ATR I strongly suggest you to build ATR libraries of your own samples and/or buy a commercial ATR library.
This point is illustrated in the figure pasted into this blog post which shows the ATR and non-ATR spectra of sucrose (table sugar). Note in the ATR spectrum (top) the peaks at low wavenumber are much bigger than the peaks at high wavenumber, whereas in the non-ATR spectrum (bottom) the peaks at low and high wavenumber are about the same size.
This phenomenon has important implications for how we use ATR spectra. Since ATR spectra look different than non-ATR spectra it is best to only compare ATR spectra to each other. This also means you will get better library searching results by only searching ATR spectra against ATR libraries. If you own an ATR I strongly suggest you to build ATR libraries of your own samples and/or buy a commercial ATR library.
Thursday, February 26, 2009
ATR II : Depth of Penetration
The depth of penetration (DP) in an ATR experiment is a measure of how far the evanescent wave penetrates into a sample. Understanding the variables that determine DP tell us a lot about how the technique works, why ATR spectra look the way they do, and the sorts of interesting applications that can be pursued via ATR. The equation for depth of penetration in an ATR experiment is (the envelope please):
DP = 1/2πWnc(sin2θ – n2sc)1/2
(please pardon the appearance of the equation, it had a rough night...and blogger does not allow subscripts and superscripts. Red is for superscripts, blue is for subscripts.)
Where
DP = Depth of Penetration (in cm)
W = Wavenumber in cm-1
nc = Refractive index of ATR crystal
θ = Angle of incidence of IR beam with crystal surface
nsc = refractive index of sample divided by refractive index of crystal
Note that all the paramaters in the DP equation are in the denominator, so when any of them goes up, DP goes down. The next several blog posts will cover the different parameters in this equation and what they teach us about the ATR experiment.
DP = 1/2πWnc(sin2θ – n2sc)1/2
(please pardon the appearance of the equation, it had a rough night...and blogger does not allow subscripts and superscripts. Red is for superscripts, blue is for subscripts.)
Where
DP = Depth of Penetration (in cm)
W = Wavenumber in cm-1
nc = Refractive index of ATR crystal
θ = Angle of incidence of IR beam with crystal surface
nsc = refractive index of sample divided by refractive index of crystal
Note that all the paramaters in the DP equation are in the denominator, so when any of them goes up, DP goes down. The next several blog posts will cover the different parameters in this equation and what they teach us about the ATR experiment.
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