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5 Disadvantages of Gas Chromatography Mass Spectrometry

5 Disadvantages of Gas Chromatography Mass Spectrometry

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Suggested Reading





























Define chromatography.

Define mass spectrometry.

What qualitative observations can you make from a TLC plate?

What is an Rf-value and how is it calculated?

Describe the procedure used to pack a column used in liquid chromatography.

Define the molecular ion peak and base peak.

How is mass spectrometry used to definitively identify a drug?

Please describe to the jury how a typical GCMS functions.

Define retention time.

What information is gained from the peaks on a chromatogram?

Is it possible for two compounds to have identical retention times? If so, describe how you would differentiate them.

Describe the difference between paper chromatography and TLC.

Cite two advantages of GCMS.

Describe the operation of a magnetic sector mass analyzer.

How is relative abundance determined using a chromatogram peak?

Describe the process of electron impact ionization.

How do you calculate a relative retention time?

Describe how a flame-ionization detector functions.

Using Table 10.2, sketch a mass spectrum for cocaine.

Refer to Fig. 10.13 and draw the ion fragments of methamphetamine produced during MS.

How can you differentiate phentermine from methamphetamine?

Cite two disadvantages of GCMS.

Describe reverse-phase HPLC. In this context, what does reverse mean?

Describe a case when a thermal conductivity detector would be preferred over a flame-ionization detector.

Provide a common analogy for the gas chromatography.

Suggested Reading

Audier, E.; Millet, A.; Sozzi, G. Mass Spectrum of Amphetamine and Related Compounds. Org. Mass Spectrum. 1984, 19, 522 – 523.

Baldwin, M. A. Mass Spectral Analysis. J. Org. Chem. 1979, 14, 601.

Bax, A. K.; Summers, M. F. Spectrometric Identification of Compounds. J. Am. Chem. Soc. 1986, 108, 2093–2094.

Crain, P. F. Mass Spectrum Review. Mass Spectrum. 1990, 9, 505–554.

De Forest, P. R.; Gaensslen, R. E.; Lee, H. C. Forensic Science: An Introduction to Criminalistics; McGraw-Hill: New York, 1983, pp. 65–68.

Dommrose, F.; Gritzmacher, H. F. Ion Processes. Int. J. Mass Spectrum. 1987, 76, 95.

Eadon, G. Mass Spectrum of Organic Compounds. Mass Spectrum. 1977, 12, 671.

Ion Exchange Chromatography. http://www.proteinchemist.com/tutorial/iec.html (accessed July 2009).

Jones, L.; Atkins, P. Chemistry: Molecules, Matter, and Change, 4th ed.; W. H. Freeman and Company: New York, 2000; pp. 10, 530–531.

Jones, M. Jr. Organic Chemistry; W. W. Norton & Company: New York, 1997; pp.686–690.

Pavia, D. L.; Lampman, G. M.; Kriz, G. S.; Engel, R. G. Introduction to Organic Laboratory Techniques, 3rd ed.; Saunders College Publishing:

New York, 1990; pp. 710–716.

Silverstein, R. M.; Bassler, G. C.; Morill, T.C. Spectroscopic Identification of Organic Compounds, 4th ed.; John Wiley & Sons: New York, 1981;

pp. 4–5.

Infrared Spectroscopy




Spectroscopy is the study of the interaction of matter with electromagnetic radiation. All forms of electromagnetic radiation

are transverse waves. This type of wave has a crest (peak) and a trough (valley) and closely resembles those commonly seen

on the ocean. The wavelength is the measured distance between two adjacent peaks or, alternatively, two adjacent troughs.

Transverse waves possess energy and anyone who has spent time in the ocean has experienced this. The amount of energy

is inversely proportional to wavelength, that is, shorter wavelengths of radiation have greater energy, while those with longer

wavelengths have less. The electromagnetic spectrum is divided into regions based on wavelength and therefore energy. The

visible region is radiation with wavelengths between 350 and 750 nm (nanometers). The energy associated with this region

differentially excites specific areas of the retina and sends a pulse down the optic nerve interpreted as color. For example, a

wavelength of 700 nm (red) has a different energy than one of 400 nm (blue). Each wavelength excites a different region of

the retina and sends a characteristic pulse through the optic nerve. Since each pulse originated from a different region, it is

interpreted as a different color.

The ultraviolet (UV) and infrared (IR) regions are adjacent to the visible section of the electromagnetic spectrum. These

wavelengths are not visible because they possess energy outside the operational range of the retina. UV radiation has a shorter

wavelength (higher energy) than visible light and is damaging to biological tissue – a characteristic that most are familiar with

and the reason for applying UV protection (SPF lotion) during prolonged exposure to the sun. Conversely, IR radiation is heat,

a low-energy form of radiation with a somewhat longer wavelength (lower energy) than visible light.

Infrared (IR) spectroscopy has been a long-established method of confirming the identity of a controlled substance.

Traditionally, the sample was subjected to a series of screening tests to establish the identity of the suspected compound and

any adulterants and diluents. The controlled substance was then extracted and purified. Finally, an IR spectrum was obtained.

Modern technology has introduced instrumentation that can obtain an IR spectrum from a single particle or from a peak in

gas chromatography (GC), thus eliminating the need for complicated extraction procedures.

IR spectroscopy requires highly purified samples, and advances in technology have drastically reduced sample preparation and analysis times. The Fourier transform IR (FTIR) spectrophotometer can obtain an IR spectrum of an individual peak

eluting off a GC column, and a micro-FTIR can isolate and obtain IR spectra of individual particles within a mixture.


Theory of Infrared Spectroscopy

IR spectroscopy relies on a compound’s ability to absorb IR radiation as a means of identification. All of the atoms in a

molecule are in continuous vibration with respect to one another. A molecule absorbs IR radiation when the frequency of a

specific vibration is equal to the frequency of the IR radiation directed on the molecule. Absorbed frequencies are recorded

and displayed as bands on an IR spectrum.

J.I. Khan et al., Basic Principles of Forensic Chemistry, DOI 10.1007/978-1-59745-437-7_11,

© Springer Science+Business Media, LLC 2012




Infrared Spectroscopy

An IR spectrum is typically a graph of percent transmittance (y-axis) versus wave numbers (x-axis). Absorbance (Abs) is

also commonly graphed on the y-axis and may be unitless or expressed in percent. The units of wave numbers are reciprocal

(or inverse) centimeters expressed as cm−1 (1/cm). This unusual x-axis label is an obvious point of confusion and requires

clarification. First, it is a matter of practical convenience. Wave numbers are directly proportional to vibrational energy and

most modern instruments are linear in the cm−1 scale. Wave numbers and frequency are terms that are often used interchangeably and, although the terms are related, this practice is not technically correct. Frequency is defined as the number of cycles

(wavelengths) that pass a given point per unit of time, usually expressed in units of cycles per second (s−1). Wave numbers

expressed in units of cm−1 are the number of wavelengths in one centimeter (wavelengths per centimeter). The concepts are

clearly related, but not identical. Both frequency and wave number are inversely proportional to wavelength; therefore, a

transverse wave of short wavelength will have a high frequency and a high wave number. Therefore, absorption frequencies

measured in IR spectroscopy can be accurately represented using wave numbers because the term is closely related to


The total number of observed absorption bands is generally quite different from the total number of fundamental vibrations. It is reduced because some modes are not IR active or a single frequency may cause more than one mode of motion to

occur. Additional overtone bands can be generated by combinations of fundamental frequencies, differences in fundamental

frequencies, and coupling interactions of fundamental frequencies. The observed intensities of overtone bands are generally

less than those of the fundamental bands. The combination and blending of all the factors create a unique IR spectrum for

each compound (Fig. 11.1).

IR radiation contains frequency ranges between 13,000 and 30 cm−1 that lie between visible light and microwave radiation

in the electromagnetic spectrum (Fig. 11.2). The area most commonly used in forensic examination lies in the middle IR

region between 4,000 and 400 cm−1. The region on the spectrum between 2,000 and 400 cm−1 is commonly referred to as the

fingerprint region.

Stretching asymmetric vibration

Stretching symmetric vibration

In-plane scissoring due to bending vibration

In-plane rocking due to bending vibration



Fig. 11.1 Common examples of

bond activity in a molecule. The

vibrations occur at characteristic

frequencies that are detected

using IR spectroscopy. Overtones

can be created by various

combinations of vibrational




Out-of-plane wagging due to

bending vibration





Out-of-plane twisting due to

bending vibration



Fig. 11.2 Infrared (IR)

spectroscopy relies on the

absorption of low-energy IR

radiation to distinguish bond

vibrational frequencies. This

analytical technique is commonly

used in forensic investigation to

confirm the presence of

functional groups in a wide

variety of drugs and controlled



Electromagnetic spectrum




Molecular rotation

quantum transition

Energy increases




Bonding electron

quantum transition


Infrared (IR)




I Molecular radiation/












Molecular rotation

quantum transition

Frequency increases



Near IR


Middle IR




Far IR




Fingerprinting region: The bands of this region are either

a group frequency or a fingerprint frequency


Infrared Spectrum

The IR spectrum is a measure of the amount of IR radiation that is absorbed by the sample. A traditional format of linear

percent transmittance (%T) versus linear wave numbers, usually from 4,000 to 400 cm−1, is used in most atlases. A 2× scale

expansion of the fingerprint region below 2,000 cm−1 is used to enhance the spectral detail of the fingerprint region.

The transmittance spectra provide better contrast between intensities of strong and weak bands because transmittance

ranges linearly from 0% to 100% T, whereas absorbance ranges nonlinearly (exponentially) from infinity to zero. The analyst

should be aware that the same sample would give quite different profiles on an IR spectrum which is linear in wave number,

compared to an IR plot which is linear in wavelength. It will appear as if some IR bands have been contracted or expanded.

The use of absorbance is not common in IR spectral atlases but is quite common in journal articles and quantitative work.

Digital databases use Abs and therefore most searches are based on Abs spectra; hence, it is becoming more widely used.

The choice of whether to display the y-axis as %T or Abs depends on the purpose at hand. It is much easier to mentally

perform the vertical mirror-image transformation of Abs to %T than it is to do the x-axis transformation of microns to wave

numbers. Quantization and search matching require Abs; however, observation of features just above the baseline seems

better in %T.

The conversion of Abs to transmittance is a simple mathematical process (Al = log (1/Tl)). Figure 11.3 demonstrates the

effect of this conversion on the spectrum.



The IR spectrophotometer is the instrument used to acquire and display the IR spectrum (Fig. 11.4). As with all modern

scientific instrumentation, the ability to obtain IR spectra has constantly improved. Despite significant advancements in

technology, there are only two basic instrument formats in common use: the dispersive instrument and the Fourier transform



Dispersive Infrared Spectrometer

Since the introduction of dispersive spectrometers in the mid-1940s, they have been widely used. Their solid design and

robust nature can withstand the repeated application of this technique.


Spectrometer Components

An IR spectrometer consists of three basic components: radiation source, monochromator, and detector. A schematic diagram of

a typical dispersive spectrometer is shown in Fig. 11.5.



Infrared Spectroscopy

Fig. 11.3 IR spectra of cocaine illustrating Absorbance and % transmittance formats. The spectra are essentially vertically flipped mirror images.

Note that high absorbance bands are reflected as low transmittance.

Fig. 11.4 A typical IR spectrophotometer. Integrated computer

workstations are used to access

the highly programmable

functions of this portable





Fig. 11.5 The complicated path of IR radiation through a dispersive IR spectrometer. A series of precisely aligned mirrors are used to direct the

beam through the various chambers of the instrument.

The IR radiation source is an inert solid, electrically heated to 1,000–1,800°C. Three of the most common types of sources

are the Nernst glower (constructed of rare-earth oxides), the Globar (constructed of silicon carbide), and the Nichrome coil.

Each source produces continuous radiation with different energy profiles.

The monochromator is a device used to disperse a broad spectrum of radiation and provides a continuous calibrated series

of electromagnetic energy bands of known wavelength or frequency range. Prisms or gratings are used to separate the radiation emanating from the source into a spectrum of wavelengths. A variable-slit mechanism, mirrors, and filters are used to

introduce bands of radiation to the sample.

The size of the slits is used to establish a balance between resolution and sensitivity during analysis. Narrow slits enable

the instrument to better distinguish more closely spaced frequencies of radiation, resulting in better resolution. Smaller slits

allow less light to reach the detector, thus reducing the sensitivity, while wider slits allow extra light to reach the detector,

providing enhanced system sensitivity. However, wider slits also expose the sample to a broader range of wavelengths,

which reduces the resolving power. Thus, a degree of compromise must be exercised when setting the desired slit size.

Most detectors used in dispersive IR spectrometers can be categorized into two classes: thermal detectors and photon

detectors. Thermal detectors measure the heating effect produced by IR radiation and include thermocouples, thermistors,

and pneumatic devices (Golay detectors). Photon detectors rely on the interaction of IR radiation with a semiconductive

material. Nonconducting electrons are excited to a conducting state that generates a small current, or voltage.

There are trade-offs with detectors as there are when selecting slit size. Thermal detectors provide a linear response over

a wide range of frequencies but exhibit slower response times and lower sensitivities. Photon detectors are more sensitive and

provide faster response times; however, their linear response over a range of IR frequencies is narrower than that found in

thermal detectors.


Spectrometer Design

In a typical dispersive IR spectrometer, radiation from a broadband source passes through the sample and is dispersed by a

monochromator into component frequencies (Fig. 11.5). The beams then fall on the detector, which generates an electrical

signal that is recorded and displayed.

Most dispersive spectrometers have a double-beam design. Two equivalent beams from the same source pass through the

sample and reference chambers, respectively. Using a sector mirror, the reference and sample beams are alternately focused

on the detector. The change of IR radiation intensity caused by sample absorption is detected as an off-null signal that is

translated into a recorder response through the actions of synchronous motors.




Infrared Spectroscopy

Limitations of Dispersive Infrared

Limitations as a result of the complex mechanics of dispersive IR are shown below:

• Slow scanning speed

• Low sensitivity to sample

• No internal reference calibration

• Insensitive to frequency by viewing one element at a time

• Sample heating and emissions from the heated sample


Fourier Transform Infrared Spectrometer

Fourier transform infrared spectrometers have recently replaced dispersive instruments for most applications because of their

superior speed and sensitivity. They have greatly extended the capabilities of IR spectroscopy and have been applied to many

areas that are very difficult or nearly impossible to analyze by dispersive techniques. Instead of viewing each component

frequency sequentially, as in a dispersive IR spectrometer, all frequencies are examined simultaneously in an FTIR spectrometer (Fig. 11.6).

Fig. 11.6 Fourier transform infrared (FTIR) spectroscopy is superior to most IR analytical techniques. The modern design of the spectrometer

has dramatically increased sensitivity, reliability, and analysis speed.


Fourier Transform Infrared Spectrometer


Fig. 11.7 The simplified beam path of IR radiation through a

Fourier transform infrared spectrometer translates to significant

reductions in maintenance and operational costs compared to

dispersive techniques.


Spectrometer Components

The three basic FTIR components are the radiation source, interferometer, and detector. Figure 11.7 shows a simplified optical layout of a typical FTIR spectrometer.

Dispersive and FTIR spectrometers use the same types of radiation sources. However, FTIR instrument sources are often

water cooled to enhance power output and stability.

FTIR spectrometers use a completely different approach to differentiate and measure the absorption at component frequencies. The monochromator is replaced by an interferometer. The interferometer divides radiant beams, generates an

optical path difference between the reflected radiant beams, and then recombines the beams. The recombination produces

repetitive interference signals measured as a function of optical path difference by the detector. The resulting interference

signals contain IR spectral information generated after passing through a sample.

The most frequently used interferometer is the Michelson, which consists of three active components: a moving mirror, a fixed mirror, and a beamsplitter. The fixed and moving mirrors are perpendicular to each other. The beamsplitter is

a semi-reflecting device often containing a thin film of germanium applied to a flat piece of potassium bromide (KBr).

Radiation from the broadband IR source is collimated and directed into the interferometer, and impinges on the beamsplitter. At the beamsplitter, half the IR beam is transmitted to the fixed mirror and the remaining half is reflected toward

the moving mirror. After the divided beams are reflected from their respective mirrors, they recombine at the beamsplitter.

An interference pattern is generated as a result of changes in the relative position of the moving mirror to the fixed mirror.

The resulting beam then passes through the sample and is eventually focused on the detector.

The detector signal is sampled at small, precise intervals during the mirror scan. The sampling rate is controlled by an

internal, independent reference, commonly a modulated monochromatic beam from a helium neon (HeNe) laser focused on

a separate detector.

The two most popular detectors used in FTIR spectrometers are deuterated triglycine sulfate (DTGS) and mercury cadmium

telluride (MCT). The response times of many detectors used in dispersive IR instruments are too slow for the rapid scan times

of the interferometer. The DTGS is a pyroelectric detector that delivers rapid responses because it measures changes in temperature rather than actual temperature values. The MCT is a photon (or quantum) detector that depends on the quantum nature of

radiation and also exhibits very fast responses. Whereas DTGS detectors operate at room temperature, MCT detectors must be

maintained at liquid nitrogen temperature (77 K) to be effective. In general, the MCT detector is faster and more sensitive than

the DTGS detector.


Spectrometer Design

The basic instrument design is quite simple. The IR radiation from a broadband source is first directed into an interferometer

where it is divided and then recombined after the split beams travel different optical paths to generate constructive and

destructive interference. Next, the resulting beam passes through the sample compartment and on to the detector.



Infrared Spectroscopy

Most bench-top FTIR spectrometers are single-beam instruments. Unlike double-beam grating spectrometers, single-beam

FTIR does not obtain transmittance or Abs IR spectra in real time. A typical operating procedure is described as follows:

1. A background spectrum is first obtained by collecting an interferogram (raw data), followed by data processing using the

Fourier transform conversion.

2. Next, a single-beam sample spectrum is collected. It contains absorption bands from the sample and the background (air

or solvent).

3. The ratio of the single-beam sample spectrum against the single-beam background spectrum results in a “double-beam”



Advantages of Fourier Transform Infrared Spectrometers

FTIR instruments have distinct advantages over dispersive spectrometers:

• Better speed and sensitivity (Felgett advantage).

• A complete spectrum can be obtained during a single scan of the moving mirror while the detector observes all frequencies simultaneously.

• Increased optical throughput (Jaquinot advantage).

• Energy-wasting slits are not required in the interferometer because dispersion or filtering is not needed. Instead, a

circular optical aperture is usually used in FTIR systems. The beam area of an FT instrument is usually 75–100 times

larger than the slit width commonly used in dispersive techniques. Thus, more radiation energy is made available. This

constitutes a major advantage for many samples or sampling techniques that are energy limited.

• Internal laser reference (Connes advantage). The use of a helium neon laser as the internal reference in many FTIR systems provides an automatic calibration with an accuracy of more than 0.01 cm−1. This eliminates the need for external


• Simpler mechanical design. There is only one moving part, the moving mirror, resulting in less wear and better


• Elimination of stray light and emission contributions. The interferometer in FTIR modulates all the frequencies. The

unmodulated stray light and sample emissions (if any) are not detected.

• Modern FTIR spectrometers are usually equipped with a powerful, computerized data system.


Fourier Transform Infrared Sample Preparation Techniques Liquid/Vapor Phase FTIR

FTIR spectra can be obtained from liquid and gas phase samples; however, these are not usually the phases of choice. The

resulting spectra have broader absorption bands which reduce the selective power of the spectra. However, vapor-phase

spectra have applications in GC/FTIR.

To obtain a gas- or liquid-phase FTIR spectrum, a background spectrum of the gas or liquid substrate is acquired. Next, a

sample spectrum is collected which contains absorption bands from the sample and the background (air or solvent). The ratio of

the sample spectrum against the background spectrum results in the spectrum of the compound of interest. Solid-Sample FTIR

Solid samples are the preferred form for IR analysis because they place the molecules into a solid crystal lattice (structure).

The fixed structure limits the ability of a functional group to vibrate, rotate, or bend. Limiting this type of movement, in turn,

limits the wavelengths of IR radiation that can be absorbed. This specificity of absorbable wavelengths leads to sharp, narrow

peaks in the IR spectra.

The crystal-lattice effect can be demonstrated through the comparison of solid-sample spectra to vapor-phase spectra. Vaporphase spectra have broader bands when compared to the solid-sample counterpart. This is attributed to the ability of the various

functional groups to more freely vibrate, rotate, or bend in the vapor phase. Figure 11.8 shows a comparison of free-base

cocaine in a solid sample (pressed KBr pellet preparation) and in the vapor phase as one would see in a GC/FTIR spectra.


Fourier Transform Infrared Spectrometer


Fig. 11.8 Comparison of cocaine samples run in solid (top) and vapor (bottom) phase. Bond vibrational modes are restricted in the solid phase

producing sharp, distinct absorption bands.

IR spectroscopy analyzes the vibrations of different parts of a molecule exposed to IR light. Changing the sample

preparation method may affect the way different parts of the molecule vibrate. This will cause shifts in the peak intensities in

the resulting IR spectra. The way the compound is crystallized (or not crystallized) within the sample matrix will affect the

resulting IR spectrum. The IR spectra of a sample crystallized within a KBr matrix (pellet) can differ from that of the same

compound directly recrystallized on a salt plate.

Polymorphism can affect a compound’s IR spectrum. A single compound may have more than one crystalline form, along

with an amorphous form (no definite structure). The way a compound crystallizes influences the vibrations within the molecule, which in turn affects the resulting IR spectrum. These variations can occur within the same sampling technique and

will result in the production of a slightly different IR spectrum.

Variations in IR spectra are somewhat influenced by sampling techniques. Therefore, a library of known spectra from

traceable sources should be maintained for compound identification purposes. The various IR spectra libraries that are available should only be used as a screening tool, not as a reference for identification. As with mass spectrometry (MS), final

identification is only accomplished by comparing the IR spectrum of the unknown to the IR spectrum of a traceable reference

standard. The spectra should be produced on the same instrument, under the same conditions.

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