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14. Analytical Chemistry (Constitutional Chemistry)

C471 Lecture
Updated: 6 November 2003


I. Introduction.

Chemists of all types need to be able to identify with certainty the substances they have made, extracted from a source, or sampled in some manner. In some cases, the species they are testing exist for very short periods of time as intermediates in chemical reactions. Whether they are trying to determine the sequences and structure of biomolecules with molecular weights in the hundreds of thousands or attempting to detect minute quantities of a small molecule that is present as a few parts per billion, analytical chemistry provides many of the tools and techniques to find the answers. Separation science is one area of concern, whether the technique be chromatography, electrophoresis, centrifugation, or some other method of separation.

Spectral databases and compilations in all ranges of the spectrum (UV/visible, infrared, microwave, etc.) as well as data compilations that result from newer spectral techniques are all available to assist in the identification of an unknown substance or the confirmation of a reaction product.

Many areas of science and technology must be called upon to perfect workable techniques for some of the problems the analytical chemist encounters. These include engineering, geology, environmental science, physics, optics, computer science, electronics, and others.

An ANALYTE is the substance to be identified, detected, or separated in some manner. A MATRIX is the sample or medium in which the analyte is analyzed.

Sometimes the searches in this area involve seeking out particular pieces of data, and other times they require the use of STANDARD METHODS of analysis to insure that chemists in diverse operating environments obtain the same results on the same samples. The methods may involve sampling techniques, sample preparation, methods to separate or purify a sample, and methods to identify a pure substance or the components of a mixture. Many of these methods are gathered in books or series that have distilled the most reliable and accurate techniques from other types of chemical publications. At times it may be necessary for the analytical chemist to create a derivative of the analyte in order to form a more volatile or more thermally stable substance that can be separated. The technique is particularly important in chromatography.

II. Encyclopedias, Dictionaries, Data Compilations, and Treatises.

Encyclopedias
The 10-volume Encyclopedia of Analytical Science (1995) covers three broad areas:

Other multi-volume works are the Encyclopedia of Analytical chemistry and the Encyclopedia of Separation Science.

The Encyclopedia of Nuclear Magnetic Resonance (1996) in 8 volumes contains 720 authoritative articles, the first 200 of which cover the history of this important technique. The encyclopedia appeared approximately 50 years after the first successful NMR experiments on condensed matter. It covers all aspects of NMR.

Among the more specialized encyclopedias that have recently appeared is the 3-volume Encyclopedia of Spectroscopy and Spectrometry (2000). Although the articles are arranged as a traditional encyclopedia in alphabetical order, the editors provide a separate contents list by topics:

Furthermore, each article is flagged as either a "Theory," "Methods and Instrumentation," or "Applications" article.

The 10-volume Encyclopedia of Mass Spectrometry was to commence publishing in 2001.

Dictionaries
A number of one-volume dictionaries appeared in the 1980s for the fields relevant to analytical chemistry, among them:

The definitive source for nomenclature of analytical chemistry is the IUPAC publication Compendium of Analytical Nomenclature (1987).

The large data compilations Beilstein Handbook of Organic Chemistry and Gmelin Handbook of Inorganic and Organometallic Chemistry contain much data of interest to analytical chemists. Now that database versions of these are available, it is easy to determine if a particular piece of analytical data exists for any of the millions of compounds in the databases. The two databases are found on the systems of the major vendors STN International and DIALOG, as well as in the versions searchable with the Beilstein CrossFire system.

Treatises
The largest continuing treatise in analytical chemistry is Wilson and Wilson's Comprehensive Analytical Chemistry. Over thirty volumes of the treatise had been published by the end of 1999. It appears that the 2nd edition of another treatise, the Treatise on Analytical Chemistry, (1978-) has stalled. The 14 volumes of the first part came out between 1978 and 1986.

III. Standard Methods, Handbooks, and Smaller Works.

One of the most popular continuing methods series is Techniques of Chemistry (1971-). The early volumes of the series were issued in a revised edition as Physical Methods of Chemistry beginning in 1986. Other specialized titles with important information for analytical chemists who work with biomolecules include Methods of Enzymatic Analysis in 12 volumes and Methods in Enzymology, a continuing series that now numbers in the hundreds of volumes. Included in the latter title are volumes that deal with basic theory, sources of equipment and reagents, and methods for DNA sequence analysis, among many others. Methods in Enzymology is now available on CD-ROM, and a related journal, Methods, is also published.

The Official Methods of Analysis of the A.O.A.C. (Association of Official Analytical Chemists) is the place to look for many of the methods used in testing substances in industry. For example, one finds here a method for determining the refractive index and water content of honey. Major sections are devoted to fertilizers, disinfectants, drugs in feeds, distilled liquors, dairy products, and color additives. Over 2,300 methods are available. Some of the types of information found in the work are:

In addition, the work has an in-depth subject index. It is available in loose-leaf or CD-ROM formats.

A much larger work, the Annual Book of ASTM Standards, appears each year with the latest word on how to test various materials. It is also good for definitions of certain industrial substances, for example, fuel oil:

ASTM Standard
D396-98 D396-98 Standard Specification for Fuel Oils.
For C471 Students ONLY, the full document can be printed from Oncourse.
(The document is found on Oncourse in 'Schedule'.)

The first volume of the ASTM set is the index. There are sections devoted to such areas as:

ASTM standards are now on the Web, and a subscription can be placed for as few as 50 copies/year. ASTM also produces the ASTM International Directory of Testing Laboratories.

Specialized works of this type include Standard Methods for the Examination of Water and Wastewater and the NIOSH Manual of Analytical Methods.

Examples of relevant handbooks are:

The last-named work includes a UV absorption index (with increasing values of λmax from 250-795 nm and the solubility in water of many stains, dyes, and indicators.

IV. Spectral Compilations.

Spectral analytical techniques encompass the full range of electromagnetic radiation. The type of radiation involved in producing a spectrum usually gives its name to the spectral technique.

Types of Spectra and the Transitions They Engender

Name Wavelengths Transitions
Radio-frequency 10-1 - 103 meters (m) Molecular rotations, NMR
Microwave 0.1 - 30 centimeters (cm) Molecular rotations, ESR/EPR
Infrared 2.5 - 50 micrometers (μm) Molecular vibrations
Visible 400 - 800 namometers (nm) Electronic excitation (atomic)
Ultraviolet 200 - 400 nm Electronic excitation (molecular)
X-ray 0.05 - 1 nm Ionization
Gamma < 0.05 nm Nuclear transitions and disintegrations

Moving down in the table above, one finds increasingly shorter wavelengths, resulting in higher energies. Thus, the energy of a given type of electromagnetic radiation is inversely proportional to its wavelength.

A spectrum may be depicted as a plot of the intensity of radiant energy emitted or absorbed versus the energy of the radiation. The energy is usually represented by the wavelength or frequency. Another method of representing spectra is to record a series of numbers that measure the peaks of the emission or absorption spectra. Either or both methods may be found in the databases and reference works that contain spectral data.

One can find new manifestations of certain types of spectra with the introduction of Fourier Transform techniques. Aldrich has libraries of both FT-NMR and FT-IR spectra.

Another spectral technique, not in the table above, is Raman spectra. These yield information by using lasers as the radiation source in the far infrared-visible region of the spectrum.

Spectroscopy also embraces the technique of mass spectrometry, wherein the instrument measures the distribution of charged particles produced after ionization, rather than radiation that is emitted or absorbed. The gas-phase ions are separated according to their masses or ratios of mass to charge (m/z). The mass spectrometer's beam of high-energy electrons thus causes organic molecules to ionize and fragment. It then separates the mixture of ions by their m/z ratios and records the relative abundance of each ionic fragment. The resultant plot of ion abundance versus m/z resembles spectra produced by other techniques.

Mass spectra are among those found in the NIST (National Institute for Standards and Technology) Chemistry WebBook, which had in its February 2000 release:

The Mass Spectrum of Isatin is reproduced below:

Isatin Mass Spectrum from NIST

In mass spectroscopy, as in other types of spectral depictions, a researcher really needs to know what types of compounds or groups yield peaks that match the measured spectrum. Most collections are indexed by the name of the compound or by molecular formula. The Important Peak Index of the Registry of Mass Spectral Data lists by m/z value the first, second, and third most abundant peaks in the Registry, covering over 50,000 compounds. The Wiley Registry of Mass Spectra Data is the largest commercially available collection of mass spectra, with over 275,000 spectra. A smaller, very popular collection of over 75,000 spectra is the NIST/EPA/NIH Mass Spectral Database.

Two companies that have produced a number of standard spectral collections are Bio-Rad Sadtler and Sigma-Aldrich.

The older printed Sadtler collections of Infrared and NMR spectra share a common index that also covers other printed compilations such as Varian and JEOL NMR sets. The references to NMR spectra in those sets are indicated by a "V" and a "J" respectively.

Checking the Sadtler Alphabetical Index for isatin, one finds:

         PRISM  |  GRATING  |     UV    |   NMR   |   C-13

Isatin 2204 | 304 | 590 | 17050 | 6606

The first two columns refer to IR spectra. Both 60 Mhz NMR and C-13 NMR spectra are covered in the indexes. Other Sadtler indexes are:

The Sadtler libraries can be purchased on CD-ROM, and there are laboratory devices that include the Sadtler collections for comparison to measured spectra in the lab. In addition, Sadtler's HaveItAll IR option offers over 200,000 spectra of pure organic and commercial compounds on one CD-ROM. It also includes 3,300 Raman spectra.

Nicolet Instruments Corporation and Galactic Instruments Corporation have developed a pay-per-use spectral library service, FTIRsearch.com. Over 71,000 FTIR and 16,000 Raman spectra are included. Other collections of electronic spectra are offered by companies such as Fiveash Data Management. SpecInfo is a database of more than 660,000 proton, C13, MS, and IR spectra that is now available on the Web. Included are the Wiley Registry of Mass Spectra and the NIST Mass Spectral Database. There is also an STN version (formerly called C13NMR/IR).

There are many reference works on spectra. You can get an idea of the range of help available by searching the terms "spectr" and "ir" in the Chemical Reference Sources Database at Indiana University. Over 50 entries are found, some of them on specific types of compounds, such as organophosphorous compounds, polymers, minerals, etc.

Despite the availability of the many compilations of spectra, it is often impossible to find a needed spectrum in any of them. Databases such as Chemical Abstracts, Beilstein, or Gmelin may then be of use in identifying a source in the primary literature.

V. Crystallography.

The Cambridge Structural Database is the largest collection of crystal structure data in the world. It covers organic and organometallic crystal structures from 1935 onward. Well over 200,000 structures are now in the file. The CSD contains bibliographic information, 2-D chemical connectivity depictions, and superb 3-D visual depictions of the molecules, as shown below in the Conquest version of the database, using the 3-D Visualiser.

CSD depiction of isatin

It has information on the preferred shapes of molecules and the preferred interactions between different molecules and organic functional groups. Both 2D- and 3D-structure searching is possible with the CSD, in addition to pharmacaphore searching. A pharmacophore is the specific 3D arrangement of functional groups within a molecular framework that is necessary to bind to a macromolecule or an active site in an enzyme.

There is also an Inorganic Crystal Structure Database.

VI. Biomolecule Sequence and Structure Databases.

The last few decades have witnessed an explosion of growth in data files associated with efforts to solve the sequence and structures of proteins, nucleic acids, and other biomolecules. Each year the journal Nucleic Acids Research has in the first issue published that year a guide to the databases of interest to molecular biologists. Categories of databases include:

The Protein Data Bank and GenBank are two of the better known databases for biomolecules. There is a service from the National Library of Medicine called Entrez that links via the Internet the relevant references from the Medline database to the databases of biomolecular sequences.

VII. The Special Review Issues of Analytical Chemistry and Other Reviews.

In alternating years, the American Chemical Society journal Analytical Chemistry published for many years special issues devoted to "Application Reviews" and "Fundamental Reviews." Applications such as air pollution, food, forensic science, particle size analysis, and water analysis are among the topics in the former, whereas thermal analysis, chemical sensors, ion-selective electrodes might be topics found in the latter. These review articles appeared for at least 50 years.

Another major review serial is Methods of Biochemical Analysis. There are lots of other review serials in the field of analytical chemistry.

VIII. Abstracting and Indexing Journals and Databases.

A large number of specialized A&I services can be found for analytical chemistry, including:

Several of the A&I services can now be had on CD-ROM or searched as online databases. Analytical WebBase (incorporating Analytical Abstracts), produced by the Royal Society of Chemistry, has comprehensive coverage for all aspects of analytical chemistry, including instrumentation and applications.

Analytical WebBase search for fuel oil as a 
matrix

Analytical Abstracts covers more than 260 journals in 12 languages, manufacturers' application notes, and Australian and British standards, as well as new books.

Link to Internet resources

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Copyright
Gary Wiggins
15 September 1996