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Articles

From the Editor

It's one thing to believe you are good at something, and another altogether to have that belief reinforced by an objective third party.

A Welcome Honor for Spectroscopy

In the U.S., the Agricultural Marketing Service (AMS) of the USDA classes cotton fiber (grades or assesses the overall fiber quality). The AMS classes U.S. cotton fiber with the Uster High Volume Instrument (HVI) (1). A key quality property measured by the HVI is cotton fiber micronaire, using an air resistance method (the cotton fiber's resistance to air flow per unit mass) (1–3). Micronaire is a function of the fiber's maturity and fineness. Although the HVI is very fast and can measure six quality parameters (including length, strength, color, trash, and length uniformity as well as micronaire), it is purely a laboratory instrument, is very expensive, and requires a tightly controlled laboratory environment. In today's global marketplace, the need exists for rapid, accurate, and precise cotton fiber measurements that can complement the HVI measurements and require less expensive instrumentation, exhibit increased flexibility and versatility, not require highly trained laboratory technicians, and perform both laboratory measurements and nonlaboratory remote (at-line or field) measurements. For cotton fiber measurements, at-line measurements are those performed in the ginning or textile manufacturing area, and field measurements are those measurements performed directly on the cotton boll in or near the cotton field.  

Near-infrared (NIR) spectroscopy methods and techniques are used extensively in the areas of agriculture, fiber, and textiles (4–8). The NIR spectral region is normally designated as covering the 800–2500 nm spectral region (primarily 1100–2500 nm) (9–11). NIR spectra represent primarily combination and overtone bands of the fundamental mid-infrared bands, primarily absorbances for the CH

, and OH chemical species. A potential major growth area for NIR spectroscopy methods and techniques is the use of portable NIR instrumentation, which could result in both laboratory and nonlaboratory analyses. The NIR measurement is a secondary measurement, and it must be calibrated to a reference method (for example, HVI micronaire). Due to the complexity of the NIR spectra, chemometric mathematical modeling often is used for instrument calibration and method development, to include multiple linear regression (MLR), partial least squares (PLS), principal component analysis (PCA), and principal component regression (PCR).  

 The "universal" nature of laboratory NIR micronaire measurements by commercial NIR units, both benchtop and portable, was demonstrated previously on a small feasibility sample set (12). It was demonstrated that portable NIR instruments could yield rapid, precise, and accurate measurements. Although the results for the portable instruments were often not as good as those obtained for the benchtop NIR instruments (normally lower 

values, higher residuals), they did readily demonstrate the potential for portable NIR instruments to measure cotton fiber micronaire. The results for the portable NIR instruments were not unexpected; the cotton fiber sample set was small and the portable instruments measured much smaller sampling areas compared to the benchtop units, and the use of a much larger and diverse set of cotton calibration samples should improve the portable NIR instrument's prediction capabilities.  

The successful development of a portable NIR method to measure cotton fiber micronaire that could be applicable to both laboratory and nonlaboratory (field or at-line remote measurements) locations was of much interest to cotton fiber producers, breeders, ginners, and textile manufacturers. These interests and previous results led to an expanded program to determine the full potential of portable NIR instruments to measure cotton fiber micronaire in both laboratory and field locations. The first phase of the program was the determination of the capabilities of portable NIR instrumentation to rapidly, precisely, and accurately measure cotton fiber micronaire in the laboratory (13,14). A comparative evaluation established the optimal instrumental settings and conditions for the portable NIR instrument. The easy-to-use, rapid, precise, and accurate portable NIR measurement of cotton fiber micronaire in the laboratory was successfully demonstrated, with high 

The second phase of the program is the determination of the capabilities of portable NIR instrumentation to rapidly and accurately measure cotton fiber micronaire in or near the cotton field, with emphasis on demonstrating and monitoring high-medium-low trends in micronaire as compared to the HVI micronaire results. At present, there is not a rapid, "as is," on-the-cotton-boll measurement of cotton micronaire. The accurate detection of micronaire trends (high-medium-low micronaire ranges within a lot) and "outlier" (low or high average micronaire) locations in the cotton field is of interest to the industry. The results for this phase are presented herein. Trend analysis is the ability of the NIR analyzer to monitor and predict the low micronaire–medium micronaire–high micronaire samples of each lot. Field analyses were made with the portable NIR instrument in four cotton fields on 15 varieties of cotton (>400 samples). Trend analyses (high-medium-low micronaire levels) and potential areas for improvements in the portable NIR field measurements are discussed.  

: For the field evaluations, fifteen lots of upland cotton samples (field–seed cotton) were obtained from four cotton fields in Mississippi and Louisiana over two years: St. Joseph, Louisiana (two fields; year 1 and year 2); Stoneville, Mississippi (year 2); and Winnsboro, Louisiana (year 2). Between 20 and 35 samples were measured with the portable NIR analyzer in or near the cotton field for micronaire, with the measurement performed directly on the cotton boll; the number of cotton bolls measured depended upon the size of the individual bolls (quantity of fiber), the condition of the field and cotton bolls, and number of plants present in the field. For measurements made in the cotton field (plant measurements), three measurements were made per cotton boll (limited battery life); for measurements made near the cotton field (vehicle measurements), four measurements were made per cotton boll. A total of 409 samples were measured and the cotton bolls were then collected for each lot of cotton. The collected samples were returned to the laboratory, conditioned, the cotton fiber ("lint"; lab/lint samples) removed by hand ("hand-ginned") from the cotton seed, NIR analyses performed on the lint samples, and the reference micronaire value obtained.  

The HVI-1000 unit at the Southern Regional Research Center (SRRC-ARS-USDA, New Orleans, Louisiana) was used to determine the micronaire reference values for all cotton samples. Five measurements were taken for each sample with the HVI unit. Because each cotton boll normally yielded 1.0–2.0 g of cotton lint, several samples had to be combined for HVI analyses of micronaire (9.5 g minimum required for the HVI unit). For each lot of cotton, the individual fiber boll samples within a lot were combined into three micronaire groups for that lot: a "high" micronaire group, a "medium" micronaire group, and a "low" micronaire group. The average micronaire value for the high-medium-low groups was different for each lot of cotton. For the 15 lots collected in the fields, 44 HVI samples were obtained (low-medium-high lots for all but one lot). The samples for each high-medium-low group for each lot were measured on the HVI system, and their micronaire results were compared to the NIR-predicted micronaire for each high-medium-low micronaire group for each lot. The field micronaire samples covered a wide micronaire range (2.78–5.86 micronaire units).  

: The Brimrose Luminar 5030 spectrometer was used in this evaluation (Brimrose Corporation of America, Sparks, Maryland). The small NIR analyzer is portable, can be battery operated in the field, and uses an acousto-optic tunable filter (AOTF) technique to measure the sample's diffuse reflectance from 1100 to 2300 nm in 2-nm increments (15). The NIR instrument used the Brimrose SNAP software (16). A sapphire glass measurement port was used so as to press the cotton fibers into a uniform surface against the instrument's port. A macro was prepared for field operations, which included the NIR micronaire calibration, spectra storage, and data storage. Using the SNAP software, each spectrum could be uploaded to a computer for further data analysis.  

: The micronaire calibration used for these preliminary field–near field evaluations was a first derivative partial least squares (PLS) cotton fiber micronaire calibration, previously developed for cotton fiber–lint and laboratory measurements (13). The micronaire calibration was developed using the Camo Unscrambler chemometric software package (Camo, Woodbridge, New Jersey) (17), and the calibration was downloaded to the NIR unit. After discussion with cotton industry representatives, mutually agreed upon measurement and performance targets or goals ("End-State Criteria") were developed. For these initial field evaluations, the end-state criteria were as follows: correct identification of broad micronaire levels (low-medium-high relative micronaire results) for greater than 65% of the field (field–seed cotton) samples; rapid analyses (less than 5 min analysis time per sample); and a user-friendly, easy-to-use method.  

Previous investigations had demonstrated the rapid, precise, and accurate measurement of cotton fiber ("lint") micronaire in a controlled environment laboratory using portable NIR instrumentation (12–14). A program was implemented to expand the NIR measurement of cotton micronaire by portable NIR instrumentation from the laboratory to a nonlaboratory location — the cotton field. This program consisted of qualitative NIR spectral analyses and quantitative NIR field evaluations to determine the feasibility of using portable NIR instruments to detect micronaire trends on cotton boll samples in or near the cotton field. 

 Figure 1: Typical NIR cotton fiber absorbance spectra, field and laboratory measurements, Brimrose Luminar 5030 portable NIR analyzer, 1100â2300 nm. 			

: Spectral analyses were performed on wide-micronaire-range cotton fiber samples, both in the laboratory and in the field, using the portable NIR analyzer. Typical cotton fiber NIR absorbance and first derivative spectra for laboratory and field measured samples are given in Figures 1 and 2. Very good NIR spectral agreement was observed between the laboratory and field measurements, with several major cotton absorption peaks and regions clearly identified in both locations. For both types of measurements, NIR spectral differences between samples with varying micronaire were observed (Figure 3). The NIR field measurements were fast (<2 min/sample) and easy to perform. 

Figure 2: Typical NIR cotton fiber first derivative spectra, field and laboratory measurements, Brimrose Luminar 5030 portable NIR analyzer, 1100â2300 nm.			

: Field measurements are the spectroscopic measurement of cotton bolls for micronaire directly on the cotton boll, in or near the cotton field. In year 1, the preliminary "sampling system" consisted of placing the portable NIR unit on the sampler's back, going into the field to the cotton plant of interest, placing the NIR unit's measuring head onto the cotton boll of interest, and taking the NIR measurement ("plant measurement"). The NIR unit's LED screen indicated the number of scans completed during the analysis, and the micronaire value was shown and recorded at the end of the analysis. A backpack harness system was developed for carrying the NIR unit into the field (Figure 4). The base unit–electronics section and batteries were placed onto the backpack frame, and the backpack was fitted onto the sampler's back. This arrangement permitted the free movement and use of the measurement component–port for NIR measurements on the cotton boll. The backpack system was shown to be a feasible method for carrying the unit into the field. The portable NIR unit and sampling system were taken to a cotton field in St. Joseph, Louisiana (LA Extension Service field). Analysis productivity was approximately 20 samples per 30 min, and the NIR system's battery life was approximately 1 h. 

Figure 3: Typical NIR cotton fiber first derivative spectra, different micronaire levels, Brimrose Luminar 5030 portable NIR analyzer, 1100â2300 nm.			

Limited battery life, operator strain (repeated bending and standing), and decreased boll sampling efficiency were observed for the plant measurement system, especially when several samples and cotton varieties were to be sampled. For future evaluations, it was agreed that a more efficient process would be to gather the cotton bolls first from the plant, take the labeled bolls to a designated location in the field (for example, the tailgate of a truck or a nearby building), and measure the samples at the designated location. In year 2, measurements were performed either in the field (plant measurement) or on the back of a vehicle in the field or at a building located next to the cotton field ("vehicle measurement") (Figure 5). The vehicle measurement increased the sampling and measurement efficiencies and the operational capabilities of the NIR unit significantly. In the vehicle measurement, the cotton bolls are collected first in the field; the bolls are taken to the vehicle or nearby building, upon which the NIR unit has been set-up for the micronaire measurements; the NIR measurements are performed; and the samples bagged and tagged for later laboratory reference micronaire analyses. Field micronaire trials with the portable NIR analyzer were performed at St. Joseph, Louisiana (LA Extension Service field); Stoneville, Mississippi (ARS field); and Winnsboro, Louisiana (LA Extension Service field). At least 20 bolls of each variety were measured. 

Field NIR Cotton Micronaire Measurements: 

Using the Unscrambler chemometric software, a laboratory micronaire calibration (PLS, first derivative) was developed for use in field evaluations. The NIR unit for field operations was operated remotely using battery power. A remote processing macro in the portable NIR unit yielded a sample number and micronaire result on the unit's display, and stored the spectral information and results for uploading to a computer for further data analysis. 

As mentioned previously, the lint samples (normally 1.0–2.0 g) of each lot  had to be combined for HVI micronaire analyses (9.5 g minimum of fiber). A total of  44 HVI samples were obtained (low-medium-high lots for all but one variety) for the 15 lots collected in the fields. The combined high-medium-low samples were measured on the HVI, and their micronaire results were compared to the NIR prediction results (average of the NIR prediction results [high-medium- low] for the individual lint bolls combined to form the high-medium-low HVI samples). The preliminary NIR-HVI micronaire results for the seed cottons measured on the boll in the field (field–seed cotton component) were very encouraging, as shown for 12 of the varieties in Figure 6. Figure 6 represents the NIR-predicted micronaire values for the high-medium-low samples of the lots displayed, with the NIR correctly detecting the low-medium-high lot trend for the displayed samples. For all 15 lots, the trends in the HVI micronaire (low-medium-high) were correctly identified for over 80% of the HVI samples. All NIR measurements were made in nonstandard conditions (temperature, relative humidity, moisture, and so forth) and on seed cotton (fiber–lint still attached to the cotton seed). When one considers that the micronaire calibration used for the field–near field NIR measurements was developed for laboratory conditions and fiber–lint micronaire analyses, the degree of NIR–HVI method agreement on micronaire trends (high-medium-low micronaire) was indeed very encouraging. 

Figure 6: NIR micronaire, fieldâseed cotton samples combined for HVI micronaire analyses. 			

In addition to the field measurements (field–seed cotton), the individual hand- ginned lint bolls (>400) were measured on the portable NIR unit before being combined. Thus, for the 15 varieties collected in the fields, the same 44 HVI samples used for the field–seed cotton comparisons were used to compare the HVI micronaire results for the combined hand ginned lint samples (lab–lint component), using the same first derivative PLS calibrations used for the field–seed cotton component. The comparative results for the lint cottons measured in the laboratory (lab–lint component) were very encouraging, as the trends in the HVI micronaire (low-medium-high) were correctly identified for 80% of the HVI samples.  

The spread or variability in the agreement between the NIR predicted micronaire and the HVI measured micronaire for the 44 combined samples was much lower for the lab–lint samples compared to the field–seed cotton samples. Thus, most of these impacts were minimized when the lint from the same samples was measured in a laboratory environment. The higher spread or variability for the field–seed cotton samples compared to the lab–lint samples was not unexpected, as the field–seed cotton results were impacted by the environmental field (nonlaboratory) conditions (temperature, relative humidity, weather conditions, and so forth). However, it is important to note that, even with these field impacts, the rapid and accurate measurement cotton fiber micronaire trends (low-medium-high) "as is" in situ, directly on the cotton boll in or near the cotton field, with a portable NIR method was demonstrated successfully. The need exists for improved chemometric models for field measurements to achieve improved NIR–HVI method agreement for field analyses. Programs are underway to improve the NIR calibrations for field analyses, to include the addition of field samples into the calibration set and the use of advanced chemometric models.  

A program was initiated to determine the capability of a portable NIR instrument to monitor the key cotton fiber property of micronaire in nonlaboratory (remote) locations, with initial emphasis on the cotton field. Portable NIR field evaluations were made at four cotton fields on 15 lot of cotton. Very good NIR spectral agreement was observed between the laboratory and field measurements, with several major cotton absorption peaks and regions clearly identified in both locations. Two field sampling systems were developed: plant measurements in which the portable NIR instrument is taken into the cotton field and NIR measurements were taken directly on the cotton plant, and vehicle measurements in which the cotton bolls were first collected and then measured with the portable NIR instrument either at the vehicle or a nearby building. Distinct micronaire differences were detected between cotton varieties and bolls with known micronaire differences. All end-state criteria were met, correct identification of broad micronaire levels (low-medium-high relative micronaire results) were observed for ≥80% of the field–seed cotton and lab–lint samples, the per sample analysis time was less than 2 min, the NIR instrument was user-friendly, and the method was simple to perform. The rapid and accurate cotton field measurement of cotton fiber micronaire with portable NIR instrumentation was demonstrated.  

The authors wish to acknowledge Ms. Jeannine Moraitis, Ms. Sarah Lillis, and Ms. Clare Kappel of SRRC-ARS-USDA for their outstanding work in performing the analyses. Ms. Lynda Tankersley of Brimrose Corporation is acknowledged for her support with the Brimrose analyzer and software.  

The use of a company or product name is solely for the purpose of providing specific information and does not imply approval or recommendation by the United States Department of Agriculture to the exclusion of others. 

 is with the Southern Regional Research Center, Agricultural Research Service, USDA, New Orleans, Louisiana; 

 is with the University of Georgia, Athens, Georgia; 

Chanel Fortier, Xiaoliang Cui, and Gayle Davidonis 

are with the Southern Regional Research Center, Agricultural Research Service, USDA, New Orleans, Louisiana; 

 is with Louisiana State University Agriculture Center, St. Joseph, Louisiana; 

 is with Louisiana State University Agriculture Center, Winnsboro, Louisiana; and 

 is with the Agricultural Research Service, USDA, Stoneville, Mississippi.  

(1) USDA AMS Cotton Program Brochure, "The Classification of Cotton," April 2001. 

(2) USDA AMS Cotton Program Brochure, "Cotton Classification, Understanding the Data," April 2005. 

 (CRC Press, Boca Raton, Florida, 2007), pp. 107–109.  

Near-Infrared Spectroscopy in Agriculture

, C. Roberts, J. Workman, and J. Reeves, Eds. (American Society of Agronomy, Agronomy Monograph No. 44, 6, Madison, Wisconsin, 2004), pp. 671–728. 

, 3rd ed., D. Burns and E. Ciurczak, Eds. (CRC Press, Boca Raton, Florida, 2008), pp. 485–520.  

 An Overview of Textile Applications of NIR Technology: Quantitative Applications

, Book of Papers of the AATCC National NIR Technology Symposium, pp. 29 (1996). 

(9) D. Burns, Modern Near Infrared Reflectance Analysis (ACS Short Course, New Orleans, Louisiana, 1985). 

, Ch. 2, 2d ed., D. Burns and E. Ciurczak, Eds. (Marcel Dekker, New York, 2001), pp. 7–18.  

(12) J. Rodgers, J. Montalvo, G. Davidonis, and D. Thibodeaux, "Analyses of Key Cotton Properties by Portable NIR Analyzers," American Association of Textile Chemists and Colorists (AATCC) International Conference and Exhibition (poster), Greenville, SC, October 2006.  

(13). J. Rodgers, G. Davidonis, V. Martin, and M. Watson, "Preliminary Evaluations of Micronaire Measurements by Near Infrared (NIR) Spectroscopy for Field Applications," Proceedings of the 2008 National Cotton Council Beltwide Cotton Conference, 1441–1446 (2008). 

(14) J. Rodgers, S. Y. Kang, G. Davidonis, and X. Cui, "Rapid Cotton Fiber Micronaire Measurements with Near Infrared (NIR) Spectroscopy — From the Laboratory to the Cotton Field," International Conference on Sustainable Textiles, Wuxi, China, October 2008.  

Article

The authors demonstrate the rapid and accurate laboratory measurement of cotton fiber micronaire trends at the cotton field with portable near infrared instrumentation.

Preliminary Field Measurement of Cotton Fiber Micronaire by Portable NIR

We have all had them — letters from a vendor of a product you are using in your laboratory that begin with the dreaded words "Dear Esteemed Customer ...." Reading those three words, you know what's coming: a price increase, your instrument will not longer be supported, your software is obsolete, the company has been taken over, or most of the above items. So what's with the title of this column, you may ask?  

Compliance with regulations or standards is an important part of my consultancy and on a few recent projects, I have had the pleasure of reviewing many examples of vendor qualification and validation documentation on behalf of clients. You might be interested to know that lifting some examples of this material is better than going to the gym. Why bother pumping iron when I can pump paper instead? However, reviewing many of these documents over a relatively short period of time, I was surprised with the following:  

The poor quality of many of these documents including the lack of scientifically sound approaches.

The misunderstanding or misinterpretation by some vendors of what the regulations actually require and, in the worst cases, providing their customers with regulatory noncompliances to explain to an inspector — for example, failure to allow users to review and approval documents before execution. 

Acceptance by laboratory staff of these documents without any critical review (it's the "if it's been written by the vendor it must be good mustn't it" syndrome).

First, to present my feedback to vendors about the quality of their documentation that they foist upon their customers, who appear to accept anything without much scrutiny or critical review. And to reciprocate all those "Dear Esteemed Customer" letters I have received over the years, now it's my turn and so welcome to "Dear Esteemed Vendor." 

Second, to educate spectroscopists and analytical chemists so that they do not accept a document at face value. Instead, they should apply their knowledge and have the confidence to be able to critically review these materials. That way they can decide if they are being given value for money or being sold, what can be called politely, agricultural fertilizer.

So we will discuss if vendor documentation for instrument qualification or computer validation meets the GXP regulations and is scientifically sound. Not prejudging the issue (very much), I will propose suggestions for you to evaluate such documentation and for improving vendor qualification/validation material. I will take this discussion wider than just spectrophotometers and also include some other instruments and systems such as balances, centrifuges, and high performance liquid chromatography (HPLC) systems that are commonly used in a laboratory.  

I want to make it clear that not all vendor qualification and validation documents are poor as there are some exceptions but unfortunately not many. Regrettably, there are many more examples which require improvements to provide customers with value for money coupled with adequate regulatory compliance, rather than generate a pile of paper simply by ticking a box. Looked at from the perspective of a regulated laboratory user, it is unlikely that you will have a single vendor for all your instrumentation, therefore you will have multiple vendors providing you with documentation for installation qualification and possibly operational qualification. So this is not just a single source problem to manage but it is a multivendor and multidocument problem to manage. From my perspective a single vendor can have a few good documents and then some poor ones so beware after a baseline has been established as that is when a poor document could catch you out. 

Over the past 20 years, it has dawned both on analytical scientists working in regulated laboratories and the regulators themselves that analytical instruments and computerized systems need to be fit for their intended use and that there must be documented evidence available to demonstrate this. This started in the early 1990s; the publication by Furman and colleagues (1) presented the FDA's viewpoint with the concept of modular and holistic qualification, Freeman and colleagues  (2) from the Pharmaceutical Analytical Science Group (PASG) gave the UK pharmaceutical industry approach with the introduction of the 4Qs model to analytical instrumentation, and Burgess and colleagues (3) looked at some of the practical issues involved with qualifying instrumentation in regulated laboratories. The UK Laboratory of the Government Chemist (LGC) developed an approach for qualification of analytical instruments (4) and then two guidance documents for HPLC systems and UV–vis spectrophotometers in the late 1990s under the Valid Analytical Measurement (VAM) program (5,6).  

However, many of the early attempts at analytical instrument qualification (AIQ) were conducted in-house but were often time consuming. So laboratories often would ask the vendors of their instruments if they could help. In principle this is a great idea, as the vendor knows their instrument, and therefore, they would be well placed to help qualify the instrument and to validate the computer system that controls it. The theory is great but the practice is often a let-down. Vendors typically have a wide market and GLP and GMP compliance is in a relatively narrow industry sector, such as the pharmaceutical or biotechnology sector. By sales, regulated laboratories can be a large market but it is small compared to the needs of the overall market requirements, from research to manufacturing, from petrochemicals to testing, from no-quality system to ISO 17025 and then to GMP/GLP. Furthermore, most vendors are certified to ISO 9001 for the delivery and support of a product or a service which can mean that documents written for compliance with ISO might not be compliant with GXP regulations. So unless a vendor specializes in this specific market sector, they can be at a loss as to understand what is required for a regulated laboratory especially as the regulatory framework has changed over the past ten years at an ever-increasing speed.  

Over time, laboratories have realized the burden, both in terms of staff time and lost work, involved in the qualification of instruments and validation of the computerized systems is too great and so various ways have been tried to reduce the impact. The development of in-house groups that will focus on qualification and validation to the laboratories (these can often be an outgrowth of existing metrology groups) was one way of helping. However, these units are often vulnerable during reorganization or merger as they are not seen as a core operation to the laboratory. This is unfortunate, as it removes from the organization the very skills required to assess and critique vendor documentation. 

The other way, providing there is a suitable budget, is to outsource to a third party such as the vendor or to a company dedicated to offering qualification and validation services for all vendor instrumentation. For the purposes of this article, I'll not consider directly the qualification services company as I wish to focus solely on vendor products and services. However, many of the principles discussed here apply equally to all documentation for qualification and validation regardless of the origin of the material. 

Vendor services to the regulated laboratory can be very lucrative, especially when times are tough, as instruments still need to be qualified initially and thereafter on a regular basis and after a major repair. So if the instrument market is down, qualification documentation coupled with delivery by professional services or the field engineers can provide a good source of revenue for an instrument company.  

It is important to understand the roles and responsibilities involved in this area. We typically have three roles to consider in qualification and validation: the system owner, quality assurance,  and the vendor.  

System Owner, typically a senior scientist who is in charge of the system in a regulated laboratory, is responsible and accountable for all qualification and validation activities carried out on the system to ensure that it is fit for purpose. The work can include qualification of an instrument, validation of the software, or both. If a portion of this work is outsourced to a third party, in this case a vendor, the vendor is responsible for carrying out the work to an agreed standard but the system owner remains accountable. 

Quality Assurance, responsible for ensuring compliance of the work and documentation with the regulations and company procedures. In Europe, there is a split documented in the regulations between QA and QC (7) that is not reflected in the U.S. GMP regulations (the Quality Control Unit or in later documents just the Quality Unit). 

Vendor who will be carrying out installation qualification and operational qualification using their knowledge of the instrument and software to install and demonstrate that the system works as expected. They will provide the documentation an the personnel to perform the qualification work.

In addition, there are two other roles with the following responsibilities:  

Laboratory Management must ensure that resources are available to qualify and validate instruments and systems as well as maintain the systems in compliance with the regulations. Resources can include time, budget, staffing, and so forth. This is consistent with the requirements of ICH Q10 on Pharmaceutical Quality Systems (8) and reflects one of the major changes in the emphasis of the GMP regulations recently.

Information Technology will also be involved if the laboratory system is to be connected to the network and can be involved if they have to supply the PC that the software will be installed on.

The basic problem is that many vendors think that they know the GXP regulations but given the evidence that I have seen when reading their documentation, this is not true. So let us look at the GMP regulations.  

In Europe, we have the GMP regulations divided into three parts plus annexes to cover specific subject areas. Part 1 covers manufacturing of products, Part 2 is GMP for active pharmaceutical ingredients and is simply ICH Q7, and Part 3 is the draft section on the Site Master File. In addition, there are 20 annexes, of which the two main ones to consider are annex 11 on computerized system validation and annex 15. It is annex 15 (9), entitled qualification and validation, that is critical to this discussion, as the vendors do not appear to have read this part of EU GMP, which has been effective since September 2001. The main clauses for this discussion are presented in Table I but please take the time to read the full annex. 

Table I: A selection of regulations for qualification and validation documentation  

Similarly, there are the U.S. GMP regulations (10) that require scientifically sound work and a document for the work being carried out under the laboratory controls sub-part of these regulations. The major sections of the U.S. GMP regulations for this discussion are presented in Table I. 

So let U.S. summarize the explicit requirements from the regulations that we need to consider further in this column. Qualification and validation documentation must meet the following:  

We need a written protocol or document that tests the instrument or system against predefined specifications (EU and U.S.).

This protocol must be reviewed and approved by the Quality Control unit in the U.S. or QA in Europe (in practice it will be QA in both regions) (EU and U.S.).

The specifications and work carried out both must be scientifically sound (EU and U.S.).

At the end of the work, there must be a report and release statement that is reviewed and approved before the next stage of work is carried out (EU).

These requirements are not the basis for negotiation, they are the law. All regulated GMP laboratories must follow them. If vendors are used they also must follow them, but, as we shall see, they rarely do, either by design or ignorance. In this the vendors are aided and abetted by naïve laboratory staff and management who also fail to appreciate some of the legal requirements of their work.  

At this point, we have not looked at 21 CFR 11 on electronic records and electronic signatures (11), however, I will return to this later in this column. I also will discuss one or two aspects of USP <1058> on analytical instrument qualification (AIQ) (12) in this column but you will need to consider the whole of this general chapter when planning any work along with any other ones applicable to the instrument you want to qualify; for example, <41> for balances, <1119> NIR, <621> chromatography, and so forth. The next "Focus on Quality" column will look at USP <1058> as it is now two years since it has been effective. It is also important to realize that there is no equivalent chapter to <1058> in the European Pharmacopoeia. 

The 4Qs model is the one that is outlined in USP <1058> (12). For those of you not familiar with the general chapter, I'll outline the four stages of the model.  

Design qualification (DQ) is the documented collection of activities that define the functional and operational specifications of the instrument and criteria for selection of the vendor, based upon the intended purpose of the instrument.

Installation qualification (IQ) is the documented collection of activities necessary to establish that an instrument is delivered as designed and specified, and is properly installed in the selected environment, and that this environment is suitable for the instrument. 

Operational qualification (OQ) is the documented collection of activities necessary to demonstrate that an instrument will function according to its operational specification in the selected environment 

Performance qualification (PQ) is the documented collection of activities necessary to demonstrate that an instrument consistently performs according to the specifications defined by the user, and is appropriate for the intended use.

The main area of the 4Qs model where a vendor can be most useful is the IQ installing their own instrument and checking it out to see it works as a system. However, as part of the outsourcing model a laboratory also can rely upon a vendor's specification for the DQ and typically will also use them for the OQ. A vendor OQ is only useful if the tests conducted match the laboratory requirements, a subject we shall return to later in this column.  

A question now arises: How good is a vendor specification? 

Does Design Qualification = Vendor Specification?

Of the four stages of the 4Qs model, the one that is performed the worst or indeed, is not performed at all, is the design qualification (DQ). The definition of DQ from earlier is "Is the documented collection of activities . . . ." Note the word activities, not activity. There is more than one in this process! However, in many laboratories, the approach is to use the manufacturer's specification. For simple instrumentation, this might be acceptable. The use of the vendor specification is enshrined in USP <1058> as being the "right" thing to do; however, read the next few paragraphs before you agree. Failure at later stages of the 4Qs model can be attributable directly to a failure to undertake an adequate DQ. So ask yourself a simple question: Have you ever purchased an instrument or system that failed to do its job? I have and so has virtually every other senior analyst. When you analyze the reason for this, it is down to the failure to specify exactly what you wanted or that you were too naïve to write a specification. 

So Let's Ask the Question: A Vendor Specification Is Good, Right?

Focus on Quality

How good is documentation supplied by a vendor to support the qualification of an instrument or the validation of a laboratory computerized system?

Dear Esteemed Vendor?

We usually think of the inside of a mass spectrometer as a "clean" environment. In interpretation of electron ionization (EI) mass spectra, we attempt to deduce rational unimolecular dissociations of ions that can be related to structure. These dissociations occur in the gas phase, isolated from the physical components of the mass spectrometer. In chemical ionization mass spectrometry (MS), controlled ion–molecule reactions occur. Again, these gas-phase reactions do not involve the surfaces of the mass spectrometer. Although heated metal surfaces can catalyze or initiate certain reactions, instruments are constructed and designed to minimize chances for such usually deleterious reactions. But these reactions can and do occur, and we do have to keep in mind the possible effects of the instrument surfaces on the quality of the measurement. Often, before considering surface-related reactions, we must confront the simple fact that the mass spectrometer gets dirty and that this dirt has an effect on instrument performance. In post-use examination of the instrument, surfaces within the ionization source and the surfaces of the mass analyzer, we find the dirt that forces us to agree that "clean" is a relative term. There are two sources of contamination within a mass spectrometer in normal operation. One source is material introduced into the instrument as sample (concentrated in the ion source), and the second source is backstreamed material from the vacuum pumps, which pervades the entire system. Both sources of contamination make the mass spectrometer a dirty place.  

Instrument operators become well aware of consequences of mass spectrometric dirt, and ionization source cleaning is periodic maintenance. When an ionization source gets dirty, observed instrument sensitivity usually decreases and focusing potentials change or become unstable. The presence of an organic layer (which can be insulating) on a metal lens surface changes the field gradient created by a focusing lens. In an EI source, the dirtiness of the source is often visually apparent upon disassembly and inspection. The filament reflector is often discolored, with a darkish, sometimes iridescent, smudge on the metal surface; this is called ion burn. The ion exit holes also are usually surrounded with a darker ion burn. This burn can build up to the point at which material actually flakes off the metal surface, confirming that the burn comes from material deposited on the surface (probably from the sample) and is not instead the result of simple heat discoloration. It is often thought that this source ion burn is the result of high-temperature oxidation of organic compounds introduced into the source. The volatilized organic compounds decompose into less volatile compounds that deposit on the source walls, although the source is usually heated to minimize adsorption. If thermal decomposition was the only process occurring, then the deposition would be uniform around the source. However, within the ionization source there is an electron beam emanating from the filament, and a more diffuse and less intense beam of ions directed to the exit slit (as well as any ions of the other polarity heading in the opposite direction). Electron- and ion-induced reactions in the gas phase can lead to sample decomposition. Of probably greater importance are reactions induced by the continual low-energy electron and ion bombardment and sputtering of organic adsorbates on the source surfaces, leading to polymerization. In the usual mode of operation of an EI source, positive ion bombardment will be concentrated at the ion exit aperture, and negative ions (not formed in equal intensity) impact the nearest positively biased surface. The observed ion burn is the end result of all of these simultaneous reactions. An analogous ion burn often is observed at the edges of lens elements or beam-defining slits adjacent to the source. These surfaces also must be cleaned regularly. 

Given the complexity of ion sources and the many different materials used in their construction, ion source cleaning is a matter of some experience, some art, and a great variety in recommended procedures. A good start can be found in articles prepared by Scientific Instrument Services (1), and, of course, more specific instructions from the instrument manufacturer. The discussion here has concentrated on EI and chemical ionization sources. Other sources also need regular maintenance, although the source of "dirt" might be different. In electrospray ionization (ESI) sources, filtering of solvents is especially important, and flow through the spray needle should be continuous to avoid the formation of precipitates in the sprayed solution within the needle. In ESI sources interfaced with trap mass analyzers, blocking the source when ions were not allowed into the trapping cell reduces the need for source cleaning (2), and off-axis spray geometries are thought to minimize blockages and fouling of ion entrance apertures. 

As described earlier, one source of the dirt that results in ion burn is the sample itself, along with carrier gases and solvents. Only a small fraction of the sample is ionized. Most of the sample is pumped away as neutral gas molecules and is transported through the high-vacuum pumps to the rough (backing) pumps. The rough pump oil eventually becomes an integrated repository for samples, serving as a holding reservoir for entrapped organic compounds, which might eventually diffuse into the exhaust stream. Rough pump oil eventually degrades with use and must be replaced; it should rightfully be considered hazardous waste. It informs our discussion of the "dirt" of MS to consider the fate of the nonionized fraction of sample. Step back to follow the route of sample introduced into a gas chromatography–mass spectrometry (GC–MS) system. Sample molecules enter a heated injection port where they are volatilized, and are then transported in a stream of carrier gas through the heated column, remaining in the gas phase as they move through the column. These sample molecules pass through a heated postcolumn interface region into a heated ionization source, hopefully remaining still in the gas phase. Those molecules that are ionized are accelerated out of the source into the mass analyzer. The majority of molecules that are not ionized are pumped out of the source into an expansive volume enclosed by surfaces that are no longer heated. The opportunity for condensation and adsorption on the postsource surfaces is high. Contamination of these surfaces and this part of the pumping system usually does not significantly impact instrument performance, but the distribution of this "dirt" should be understood in a practical sense. The source rough (backing) pump often needs more regular maintenance than do the other backing pumps, and its exhaust should certainly be filtered and directed to a fume hood.  

Our attention now turns to the sample molecules that are ionized. In a through-space instrument, these ions travel from the source through the mass analyzer, eventually to be destroyed (and converted to an electrical signal) at the detector, whether it is an electron multiplier, a photomultiplier, or some other transducer. At each stage in transit through the instrument, various losses deplete the ion current. When the "lost" ions encounter a surface (such as the inner surface of a flight tube or a quadrupole rod), they are neutralized. They can become gas that is pumped away immediately, or they can be deposited as part of the adsorbed organic film on that surface. In the analysis of radioactive samples, it can be shown that eventually all inner surfaces of the mass spectrometer become coated with radioactive residue. A unique procedure to reduce the background signal obtained by radioactive ions implanted into the first dynode of the electron multiplier has been described (3). It is of interest here that the sample in one instance becomes contamination in the next. The take-home lesson is that sample ions, in time, become distributed throughout the entire instrument.  

Consider, in a very broad sense, production of ions in the ionization source. A general goal is that all ions produced in the source are accelerated into the mass analyzer. This population of ions might contain many ions outside the mass range scanned by the analyzer. For example, many scans have a lower mass limit of 50 so that intense ions at 

 28, 32, 40, and 44 (background ions from residual air) or ions representative of a chemical ionization reagent gas are not recorded in each mass spectrum. The contribution of these ions to the total ion current from the source can be substantial and far more intense than ions derived from any sample. We don't usually consider such ions as dirt or contamination, and often, we don't even consider them at all. However, they do contribute to sputtering and polymerization processes of adsorbates on metal surfaces, even though they might not directly be a source of residue on those surfaces. 

We'll next trace the paths of ions that pass into the mass analyzer through a quadrupole mass filter and the sector mass analyzer. Principles of operation for the quadrupole mass filter are described in introductory texts (4). The quadrupole mass filter operates by creating electric fields such that, at any given instant (and set of electric fields), ions of only one mass follow a stable trajectory through the entire length of the rod assembly. Other ions of different masses follow unstable trajectories, meaning that they exit the rod assembly, or more likely, collide with one of the rods. Most of those collisions occur near the source end of the rod structure, and it is here that ion burn is often observed (Figure 1). In the past, the shape of these burns and their symmetry have been linked to the profile of the ion beam and the process of its mass analysis. But the observed ion burn is the result of millions of ion collisions, subsequent sputtering processes, and so many other convolved reactions that it is best not to over-interpret the pattern. A consequence of ion burn on the quadrupole rods is sometimes seen in the shape for an ion beam, appearing as a lift off on one side of the peak. The ion burn is often semi-insulating and changes the symmetry of the electric fields otherwise generated by the rods. As noted earlier, the ion burn can be formed primarily by intense ions outside the scanned mass range. But it should also be remembered that the quadrupole mass filter operates by passing through to the detector only one mass ion at any instant. All of the other ions from the sample follow unstable trajectories. At any instant during a scan across the mass range, the device is discarding most of the ions derived from the sample. Certainly, in a selected-ion monitoring experiment, only the selected ions pass through to the structure, all other ions of other masses are discarded. It should come as no surprise that the rods become dirty and that a visible ion burn results. Although some part of the ion burn derives from sample ions, it is also partly the result of ion bombardment of contaminant material adsorbed onto the quadrupole rod, as discussed later. 

 Figure 1: Ion burn on the front end of quadrupole rods. The burn usually appears on all four rods, but it may not be symmetric. The size and shape of the ion burns should not be over-interpreted.  

In a sector-based mass spectrometer, the (usual) scan of the magnetic field strength means that, at any given instant, only ions of one particular mass are making it through to the detector. Ions of other masses will collide with the inner surfaces of the flight tube. But their distribution is spread over a much greater surface area than in the quadrupole mass filter, and so a distinct "ion burn" is not usually seen on these surfaces. Should one disassemble a sector mass spectrometer and swab the inner surfaces of the flight tube, some visible residue usually can be seen. But this is not dirt of the same sort as an ion burn. Given the pressures at which most mass spectrometers operate, the interior surfaces of the instrument itself are covered by layers of adsorbed gases and system contaminants. The adsorption and desorption of gases on metal surfaces as a function of temperature and pressure are well-studied phenomena. Surface science research on clean surfaces (such as with secondary ion mass spectrometry) usually involves operation at 10

  Torr pressure of the ordinary organic mass spectrometer seems, by comparison, to be an organic soup. The old saying, "One scientist's vacuum is another one's sewer," although meant to be humorous, is not inaccurate. We'll use the general term "contaminant" for any of the many organic adsorbates that can be found on an otherwise "clean" metal surface inside a mass spectrometer.  

The major source of this adsorbate contamination within a mass spectrometer derives from the pumping system (5). Backstreamed oil from diffusion pumps, turbomolecular pumps, and transfer of lubricants from other moving parts within the system will inevitably find their way into the main vacuum chamber and distribute throughout the system. Vacuum system devices designed to decrease the flux of backstreamed vapors include baffles and cold traps, and the importance of proper operation in bringing a system to atmospheric pressure and pumping it down afterwards must be foremost. Considering that some degree of contamination is inevitable, many instruments, including larger sector instruments, include provisions for a bakeout. In the bakeout process, the instrument is jacketed in an insulating cover and the internal metal surfaces are heated to a high temperature while still under vacuum to force desorption of adsorbates. It is especially important to heat the instrument uniformly, as any desorbed gases will find a cold spot in the system and condense upon it. Vacuum science provides sophisticated tools assembled into a balanced system, all with the same goal of moving gas molecules from inside the vacuum chamber to the outside world. But realistic vacuum science deals with leaks, and these occur at every flange and every feedthrough. Lower and lower ultimate pressures are achieved within the system when the pumping speed exceeds the flow rate of leaks into the system. But even pressures that appear to be steady represent a dynamic equilibrium, and the presence of contaminants in the system, including the samples themselves, is a given. Sensitive as the instrument might be, the mass spectrometer is a dirty environment indeed. 

Ions that do transit the entire mass spectrometer finally reach the detector. In the dynode electron multiplier detector, the high-velocity impact of a positive ion at the entrance dynode of the multiplier releases electrons that are accelerated to the next dynode, releasing still more electrons in a cascading process. In much the same manner that ion burn can appear elsewhere in the mass spectrometer, the electron multiplier itself can be contaminated, and processes have therefore been devised to clean and rejuvenate such devices. Many modern instruments use a phosphor and photomultiplier tube combination as a detector, because this arrangement can be less susceptible to decreased performance due to contamination.  

On a final note, "ion burn" is also a technical term used to describe the visible spot on a cathode ray tube, as used in an old television or scope, representing damage to the coated layer. An authoritative review of this phenomenon by Sloane and Watt in 1948 (6) is especially interesting in that it describes the extensive use of MS to attempt to identify the positive and negative ions thought to be present in the system. 

 thanks Jonathan Batey and Bob Bateman for discussions of the phenomenon of ion burn. He is amused that a web search for "ion burn" leads to many sites that describe a phenomenon observed in older cathode ray tubes such as those used in the early days of television. Because many of those web sites are presented in a historical sense ("this technology is SO old!"), he is not quite so amused that he remembers such TV ion burns from first-hand experience. This column is the sole responsibility of the author, who can be reached at 

(2) SA. Hofstadler, K.A. Sannes-Lowery, and R.H. Griffey, 

(3) F. Touchard, G. Huber, R. Fergeau, C. Thibault, and R. Klapisch, 

Quadrupole Mass Spectrometry and Its Applications

http://www.vacuumlab.com/Articles/Oil-Sealed%20Pumps%20and%20Backstreaming.pdf

Mass Spectrometry Forum

Ken Busch explores the dirt of mass spectrometry ? its origins and its visible consequences in a deposit on metal surfaces called ion burn.

Ion Burn and the Dirt of Mass Spectrometry

Fourier transform–infrared (FT-IR) spectroscopy has become a very popular technique because of its ability to analyze such a broad range of chemicals and compounds. Its application to microscopy and the subsequent development of imaging FT-IR have also found numerous uses. Technological improvements have resulted in the development of the FT-IR imaging market into a significant segment of the overall FT-IR spectroscopy market. 

 FT-IR imaging demand by industry for 2009.			

FT-IR microscopes are useful because they are able to characterize very small regions of a sample, which is of value when the inspection of a small defect, inhomogeneity, or feature on a sample is required. However, these areas of interest on a variety of types of samples can be much larger, and mapping of the sample provides far more helpful information for research or quality analysis. While more conventional microscope instruments can perform limited mapping applications, they are quite slow. The development of imaging FT-IR systems, which can map samples much more quickly, was hindered initially by the limitations of current detector and electronics technology. Over the past decade, FT-IR imaging systems have overcome such limitations to offer robust instruments with performance comparable to conventional microscopy and spectrophotometer systems. 

   In 2009, the global market for FT-IR imaging systems was about $30 million, and it is expected to see growth slightly higher than for conventional FT-IR microscopes, despite the relatively high cost of imaging systems. The analysis of pharmaceutical tablets remains one of the key applications, but analyses of polymer coatings, semiconductors, biomedical samples, and forensics analysis have also become major uses for the technique. 

   The foregoing data were extracted from SDi's market analysis and perspectives report titled "The Global Assessment Report 11th Edition: The Laboratory Life Science and Analytical Instrument Industry," September 2010. For more information, contact Stuart Press, Vice President, Strategic Directions International, Inc., 6242 Westchester Parkway, Suite 100, Los Angeles, CA 90045, (310) 641-4982, fax: (310) 641-8851, 

Market Profile

Fourier transform–infrared (FT-IR) spectroscopy has become a very popular technique because of its ability to analyze such a broad range of chemicals and compounds.

Market Profile: FT-IR Spectroscopy

In the last installment about group theory (1), I introduced character tables as the simplest representation of the behavior of the symmetry operations of a group. All well and good, but how are they used? 

It is not unusual in applying group theory to come across a set of characters in a particular point group that do not belong to one of the irreducible representations. One such set of characters in a system with 

 symmetry is shown in Figure 1, where we are using "Γ" as the general symbol for a reducible representation. How do we know that this representation is reducible? Easy, we just look at the character table for 

 (Figure 2) and note that this set of numbers is not listed in the character table. Because it's not an irreducible representation, it must be a reducible one. (NB: Any representation in any point group will either be irreducible or reducible. If it is not, then it has been constructed incorrectly.) 

Figure 1: Set of characters with C2v	 symmetry. 

We need to separate this reducible representation into its irreducible components. This is the equivalent of denoting any point in three-dimensional space as so many 

. Only in this case, our "basis" is not composed of 

; it's composed of the irreducible representations of the point group. In this case, we would write the appropriate combination as 

 represent the number of each irreducible representation in the reducible one, and the symbol "⊕" means "direct sum." A direct sum is the sum of the characters of each symmetry element to generate a new set of characters. Characters from different symmetry elements are never combined. Separating a reducible representation into its irreducible counterparts is called, naturally, reducing the reducible representation.

We might be able to reduce it by inspection; that is, figure it out by looking at Figure 2 and maybe do a little bit of trial and error. That may work for low-magnitude reducible representations, but it's much more difficult for larger ones. What we really need is a systematic way to reduce a representation. 

Figure 2: Character table for the C2v point group.  

The standard way to reduce a reducible representation is to use the Great Orthogonality Theorem, sometimes also known as the Grand Orthogonality Theorem but in either case abbreviated the GOT (2): where

 is the number of times a certain irreducible representation appears in a reducible one;

 is the number of symmetry elements in the point group (known as the 

 is the number of symmetry elements in each column of the point group, which are known as classes; χ

 is the character of the reducible representation, and χ

 is the character of that irreducible representation. This expression is evaluated for each irreducible representation in the character table, and the 

 values are always integers ranging between zero and the highest character in the reducible representation (usually the character for

E, the identity element). If it's not an integer, an error has been made. The GOT is one form of the Schur orthogonality relations, which are some general orthogonality relationships for mathematical groups and are named after Issai Schur, an Eastern European mathematician who specialized in mathematical groups. (I say "Eastern European" because he was born in what is now Belarus, grew up in what is now Latvia, and was educated and worked in Germany.) 

Let us see how the GOT works by reducing the reducible representation above. To determine how many times A

 appears in our reducible representation, we combine the characters of A

 with the characters from the reducible representation, multiply by the number of symmetry elements in each class (which, from Figure 2, is just 1 for each symmetry element), and sum over all classes of symmetry elements before dividing by the order of the group, which is 4: 

The numbers inside the square brackets are, respectively, the number of elements in each class (each column of the 

 point group only has one symmetry element), the character of each class for A

, and the respective character in each class from Γ. Determining the 

 for the other three irreducible representations in Γ: 

So, this irreducible representation reduces into a combination of 1 A

 irreducible representations. We write this as this direct sum:  

We have reduced this reducible representation into its irreducible equivalent. 

There are several applications of the GOT in the chemical sciences (2,3). Here I will focus on two: the symmetry descriptions of molecular vibrations and the partial determination of the value of an integral. 

 possible net motions of its nuclei (each nucleus can move in three dimensions, hence the 3

 motions, three are the translations of the molecule as a whole and three are the rotations of the molecule about its center of mass (two, if the molecule is linear). The remaining 3

 – 5 if linear) motions are movements of the atoms of the molecule that do not move the center of mass of the molecule. They are called vibrations. 

The random possible motions of the vibrations of a molecule can be broken down (dare I say, reduced) into fundamental motions called the normal modes of vibration. It's the normal modes of vibration that are measured when a vibrational spectrum is measured. The normal modes of vibration represent the most basic description of the vibrations of a polyatomic molecule. (Individual atoms don't have vibrations; in the solid state, the motions of the particles with respect to other particles, whether they be atoms or molecules, are called phonon modes and are considered separately from the vibrations.) 

When the symmetry of a molecule is determined, the nuclear motions of the atoms that make up the vibration are ignored; however, each vibration works to distort the apparent symmetry of the molecule. On average, however, the molecule still has the symmetry as determined by non-moving nuclei. The possible motions of the molecule, however, can be used to generate a set of characters that describe the 3

 motions under that symmetry point group. This character set can be reduced using the GOT. Of the set of irreducible representations, three of them correspond to the translations, and three (or two, if linear) correspond to the rotations. The remaining 3

 – 5) irreducible representations stand for the vibrations. Each vibration of the molecule can be labeled with an irreducible representation of the point group. 

Figure 3:  Reducible character set for a C2v	 molecule that has three atoms.  

There are various standard recipes for generating the character set for the motions of any given molecule (see references 2–4). In most cases, the set of characters is reducible but is difficult to reduce by inspection (except maybe for two- or three-atom molecules). Thus, the GOT must be used to reduce it and to remove the translational and rotational parts. 

Figure 4:  An expanded character table for the C2v	 point group.  

O) gets the  reducible character set shown in Figure 3. Can you reduce this by inspection? Likely not (no offense intended!). However, using the GOT, we can determine that this reducible representation reduces to: 

To remove the translational and rotational motions, we need additional information. This information is usually found in an expanded character table, shown in Figure 4. The "R" entries list the irreducible representations that are assigned to rotations in 

 entries list the irreducible representations that are assigned to the translations in 

 must be removed from Γ to account for the rotations, and an 

 irreducible representation must be removed to account for the translations. What is left over are the irreducible representations that must be assigned to the normal modes of vibration. We have 

Thus, the three normal modes of vibration are assigned two A

 label. For small molecules it is easy to assign these labels by inspection, as the characters of each irreducible representation represent eigenvalues of the motion vectors as the symmetry operation is applied the individual vibration. For larger molecules, a more detailed approach is necessary to assign labels to the vibrational modes; the details of doing this are beyond our scope but can be found in some classic books (5). 

The second use of the GOT comes with evaluating transition moments. In spectroscopy, a transition moment 

 is the wavefunction of the upper state, Ψ

 is the wavefunction of the lower state, and µ is the dipole moment operator. In a system of a given symmetry, the two wavefunctions and the operator can be labeled by irreducible representations, just like vibrations are. The overall set of characters for the integrand is the product of the irreducible representation's characters of the three functions in the integrand: 

The "⊕" symbol now represents the direct product in which the characters from each symmetry element are multiplied by each other (rather than added, as we found in the direct sum). The multiplication of characters generates a new character set that is the representation of the integrand as a whole. 

A transition moment is a number. It may be zero, it may be nonzero. However, for it to be nonzero, Γ

 must be or contain (by reduction by the GOT) the all-symmetric irreducible representation of that point group. The all-symmetric irreducible representation is the one that contains all ones as characters; it is typically labeled A

 but may be labeled as "A-something else" in some character tables. It is always listed first in a character table. 

Why is this so? Because if the transition moment is nonzero, it has some finite value, and it is not a vector. A numerical value must be invariant to any possible symmetry operation, which means its eigenvalue for any symmetry operation must be 1. This means that, if you are taking the character as an eigenvalue, the symmetry of the integrand must include the all-symmetric irreducible representation as part of its character set. Sometimes you can tell by inspection, but in other cases you have to use the GOT to reduce the reducible representation, just like we did for the vibrations above. If A

 (or however the all-symmetric irreducible representation) is NOT part of Γ

, then the integral must equal to zero. Only if A

 can the integral be nonzero (however, the symmetry considerations give no hint about how nonzero the value will be). 

These irreducible representation-based conclusions are the basis for selection rules. In cases where A

 is not present, the spectroscopic transition is predicted to not occur and is considered forbidden. If A

 is present, then the spectroscopic transition is allowed. Knowing even approximate wavefunctions allows us to determine what selection rules will be, typically in terms of the change of the relevant quantum number. 

I hope you have enjoyed our multi-part foray into symmetry and group theory. It is a fascinating subject, one that all spectroscopists should be familiar with. Hopefully this series has inspired you to look further into a field of mathematics that is very important in spectroscopy. 

 is a professor of chemistry at Cleveland State University in Ohio. Many of his "Baseline" columns have been reprinted in book form by SPIE Press as 

 available through the SPIE Web Bookstore at 

 was published in May 2006 and is available from SPIE Press. He can be reached at 

Here, we continue our treatment of symmetry and group theory by introducing a very useful mathematical tool in group theory. It has two names in common use, but thankfully they both have the same acronym: GOT.

Spectroscopy-09-01-2010

A Welcome Honor for Spectroscopy

Preliminary Field Measurement of Cotton Fiber Micronaire by Portable NIR

Dear Esteemed Vendor?

Ion Burn and the Dirt of Mass Spectrometry

Market Profile: FT-IR Spectroscopy

Group Theory and Symmetry, Part IV: Great or Grand, We've Got GOT

Products

Vol 25 No 9 Spectroscopy September 2010 Regular Issue PDF