Chemical Information Sources/Analytical Chemistry Searches
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 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 ensure 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 in which are 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.
Encyclopedias, Dictionaries, Data Compilations, and Treatises
All of the encyclopedias mentioned here, except the Encyclopedia of Mass Spectrometry, are available in both print and online versions, which require purchase or subscription.
The 10-volume Encyclopedia of Analytical Science (2nd ed., 2005) covers three broad areas:
- techniques (e.g., spot tests, mass spectroscopy, chromatography, immunoassays)
- field or material of application (e.g., forensic science, food analysis, ceramics, pharmaceuticals)
- analytes (e.g., mercury (speciation), glucose, nucleic acids, pesticides)
The Encyclopedia of Analytical Chemistry, originally published in 15 volumes in 2000, covers theory, instrumentation, applications, and techniques. It is updated periodically with online articles. Those articles appearing in 2008-2010 have also been published in a three-volume supplementary set that includes proteomics, genomics, imaging technology, and nanotechnology.
The 10-volume Encyclopedia of Separation Science (2000) is organized around three levels of information:
- Overviews of the theory of 12 categories of separation techniques (e.g., distillation, electrophoresis, membrane separations)
- Detailed theoretical and technical descriptions of specific techniques (e.g., gas, liquid, supercritical fluid, and thin-layer chromatography)
- Specific applications of techniques, including micro and macro, lab bench and industrial applications (e.g., solid-phase microextraction, chiral separations, flotation of ores, ion exchange for water treatment)
The Encyclopedia of Nuclear Magnetic Resonance (8 volumes in 1996, volume 9 in 2002) contains 786 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, with volume 9 covering advances since the first 8 volumes. The electronic version is entitled Encyclopedia of Magnetic Resonance and is updated periodically with new online articles.
Among the more specialized encyclopedias that have recently appeared is the Encyclopedia of Spectroscopy and Spectrometry (2nd ed, 2010) in three volumes. It covers theory, methods, and applications. Although the articles are arranged as a traditional encyclopedia in alphabetical order, the editors provide a separate contents list by topics:
- Atomic Spectroscopy
- Electronic Spectroscopy
- Fundamentals of Spectroscopy
- High Energy Spectroscopy
- Magnetic Resonance
- Mass Spectrometry
- Spatially Resolved (and other Structural) Methods
- Vibrational, Rotational & Raman Spectroscopies.
Furthermore, each article is flagged as either a "Theory," "Methods and Instrumentation," "Applications," or "Historical Overview" article.
As of 2012 seven volumes of the projected 10-volume Encyclopedia of Mass Spectrometry had appeared. Existing volumes cover Theory and Ion Chemistry, Biological Applications, Organic and Organometallic Compounds, Elemental and Isotope Ratio Mass Spectrometry, Ionization Methods, and Hyphenated Methods.
A number of one-volume dictionaries appeared in the 1980s for the fields relevant to analytical chemistry, among them:
- A Dictionary of Spectroscopy (2nd ed., 1982)
- A Dictionary of Chromatography (2nd ed., 1982)
- A Dictionary of Electrochemistry (2nd ed., 1984)
- A Dictionary of Concepts in NMR (1989, revised 1992).
The definitive source for nomenclature of analytical chemistry is the IUPAC publication Compendium of Analytical Nomenclature (The Orange Book) from 1997 (3rd ed.). IUPAC also maintains a web version on its web site.
The largest continuing treatise in analytical chemistry is Wilson and Wilson's Comprehensive Analytical Chemistry, now also available online. It appears that the 2nd edition of another treatise, the Treatise on Analytical Chemistry, (1978-) has stalled. Only 12 of 14 volumes of Part I came out between 1978 and 1993.
Standard Methods, Handbooks, and Smaller Works
The Official Methods of Analysis from AOAC INTERNATIONAL (formerly the 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 methods for determining moisture in honey and cadmium in earthenware. With the 18th edition (2004) the OMA is also available online as a "continuous edition" that is updated as soon as new and revised procedures are approved and ready. It is searchable by analyte, matrix, equipment or technique, method number and approving body, as well as full-text keywords. Previous print editions were published under variations of the title Official Methods of Analysis of the A.O.A.C with annual loose-leaf updates between editions. There is an in-depth subject index.
AOAC evaluates chemistry, microbiology, and molecular biology methods, and more than 2,300 are available. Major topics covered include fertilizers, disinfectants, drugs in feeds, distilled liquors, dairy products, and color additives. Some of the types of information found in the work are:
- Apparatus and reagent specifications
- Cautionary notes referring users to safety information
- Methods titles that include analytes, matrixes, methodologies used and cooperating organizations where applicable
- Applicability statements with limitations of methods
- References for appropriate collaborative studies and subsequent revisions
- Chemical and common names of all drugs and pesticides
- CAS Registry Numbers where applicable.
AOAC also publishes the Journal of the AOAC INTERNATIONAL and AOAC INTERNATIONAL Guidelines for Laboratories Performing Microbiological and Chemical Analyses of Food and Pharmaceuticals, as well as relevant books.
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. The first volume of the ASTM set is the index. There are sections devoted to such areas as:
- Section 1. Iron and steel products
- Section 4. Construction
- Section 5. Petroleum products, lubricants, and fossil fuels
- Section 8. Plastics
- Section 14. General methods and instrumentation.
ASTM standards are now on the Web, and a subscription can be placed for as few as 25 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.
A popular, but now discontinued, methods series is Techniques of Chemistry (1971- 1995). The early volumes of the series were issued in a revised edition as Physical Methods of Chemistry from 1986 - 1993. 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 online, and a related journal, Methods, is also published.
Examples of relevant handbooks are:
- Analytical Chemistry Handbook (2nd ed., 2004)
- Handbook of Basic Tables for Chemical Analysis (3rd ed., 2011)
- US Pharmacopeia/National Formulary (annual)
- Reagent Chemicals (10th ed., 2005)
- Dictionary of Analytical Reagents (1993)
- The Sigma-Aldrich Handbook of Stains, Dyes, and Indicators (1990).
The last-named work includes a UV absorption index with increasing values of λ-max from 250-795 nm and the solubility in water of many stains, dyes, and indicators.
Various governmental agencies such as the U.S. Environmental Protection Agency (EPA) and the National Institute of Occupational Health (NIOSH) publish individual and compendiums of analytical methods related to their regulatory activities. Although many of these were issued in print, these are now typically published on the internet, giving some assurance of their currency. Two examples are EPA's Clean Water Act Analytical Methods site and the NIOSH Manual of Analytical Methods.
Large Data Compilations
The large classic print data compilations Beilstein Handbook of Organic Chemistry and Gmelin Handbook of Inorganic and Organometallic Chemistry contain much data of interest to analytical chemists. Database access makes it easier to determine if a particular piece of analytical data exists for any of the millions of compounds covered, and the content of both handbooks is now included online in Reaxys. Similarly, the SciFinder database that includes the REGISTRY compound database (Chemical Abstracts Service) increasingly provide access to both experimental and computed data and spectra as well as many literature references to analytical techniques.
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
|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, and the electronic Sigma-Aldrich chemical catalog includes links to spectra for many compounds.
Another spectral technique, not in the table above, is Raman spectroscopy. This yields 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 of Standards and Technology) Chemistry WebBook. As of June 2005, the last release before switching to ongoing incremental updates, the WebBook contained:
- IR spectra for over 16,000 compounds
- Mass spectra for over 15,000 compounds
- UV/Vis spectra for over 1,600 compounds
- Vibrational and electronic energy levels for over 5,000 compounds
- Constants of diatomic molecules (spectroscopic data) for over 600 compounds.
In mass spectrometry, 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 Spectral Data is the largest commercially available collection of mass spectra. In 2011, Wiley introduced, in association with eMolecules, ChemGate. This web resource, no longer available, enabled a search by structure of 500,000 compounds to find NMR, IR, or Mass spectra. Wiley bundles NMR spectrum prediction with the NMR collections (13C, 15N, 17O, 19F, 31P, 1H), based both on algorithm prediction and machine-learning prediction (via training on the included databases).
Wiley Carbon-13 NMR and Mass spectra images are now included in the data associated with entries in the CAS Registry File. The Registry File also has IR absorption spectra from the Japanese Spectral Database for Organic Compounds.
A smaller, popular collection of over 240,000 spectra is the NIST/EPA/NIH Mass Spectral Library with Search Program, available through various distributors.
Two companies that have produced a number of standard spectral collections are Bio-Rad and Sigma-Aldrich. Bio-Rad Laboratories encompasses the Sadtler suite of spectra long held by many libraries in printed format. An often overlooked place to find your spectrum is the local analytical chemistry laboratory, which likely has some or many of the large libraries installed on the spectrometers (e.g. Wiley Registry, NIST, Bio-Rad, etc.). Some of these libraries are quite large.
Bio-Rad's KnowItAll Informatics System is an integrated software and database package that provides tools such as database building, management, search, analysis, prediction, structure drawing, and reporting within a single user interface. Academic institutions may obtain a license for KnowItAll U that includes a collection of software tools and over 1.4 million spectra:
- All Bio-Rad Sadtler spectra
- over 330,000 IR, NMR, Raman, UV-Vis, and mass spectra
- Most John Wiley & Sons spectra
- over 838,000 IR, NMR, and mass spectra
- All spectra of Prof. Dr. Wolfgang Robien / Universität Wien
- 281,000 NMR spectra
- KnowItAll Informatics System
- KnowItAll AnyWare
- A web browser-enabled client that is hardware, operating system, and browser independent, allowing access to the KnowItAll U database collection via Windows, Macintosh, or Linux
A free KnowItAll Academic Edition for faculty and students is a software package for drawing 3-D structures, importing spectra into reports, interpreting spectral bands, and more.
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:
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:
- Cumulative Chemical Class Index
- Cumulative Molecular Formula Index
- Cumulative Molecular Weight Index
- Cumulative Numerical Index
- Cumulative Spec-Finder Index.
Nicolet Instruments Corporation (now Thermo Scientific) and Galactic Instruments Corporation developed a pay-per-use spectral library service. FTIRsearch.com provides access to approximately 71,000 FTIR and 16,000 Raman spectra from the Thermo Scientific and Sigma/Aldrich libraries. Other collections of electronic spectra are offered by companies such as Fiveash Data Management. SpecInfo is a database of more than 660,000 proton, C-13, MS, and IR spectra that is now available on the Web via Wiley Online Library. Also available is the Wiley Registry of Mass Spectral Data , as previously noted. Compound coverage can be verified at Compound Search.
SDBS, the Spectral Database for Organic Compounds, is a free website from the National Institute of Advanced Industrial Science and Technology (AIST) in Japan. It provides access to IR, NMR, MS, Raman, and some ESR spectra.
ChemSpider is another free resource. It provides property, identification, and other information for over 28 million chemical structures from hundreds of sources. Types of spectra that may be available include IR, proton and C-13 NMR, electron impact, mass spectra, and UV-Vis. The database is searchable by name, structure, CAS registry number, and identifiers such as SMILES and InChI.
There are many reference works on spectra. You can get an idea of the range of resources by referring to spectra guides maintained by major academic libraries such as the University of Arizona, Stanford University, or the University at Buffalo.
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 SciFinder (Chemical Abstracts) or Reaxys may then be of use in identifying a source in the primary literature. In fact, the CAS Registry database now includes more than 1.1 million experimental spectra for 816,000 substances. In 2009, this comprised:
- More than 408,000 proton, carbon-13, and heteroatom NMR
- More than 127,000 mass spec
- Nearly 174,000 IR
- Nearly 3000 Raman spectra.
Some of these are from Wiley, some from BioRad, some from AIST: Integrated Spectral Database System of Organic Compounds (Japan), and some are references to spectra in the literature.
The Cambridge Structural Database is the largest collection of crystal structure data in the world, with over 500,000 structures. It covers organic and organometallic crystal structures from as early as 1923. The CSD contains bibliographic information, 2-D chemical connectivity depictions, and superb 3-D visual depictions of the molecules and unit cells through a choice of online viewers.
The CSD is part of the CSD System, which includes software for searching, structure visualization, statistical analysis, and database creation. It also has information on the preferred shapes of molecules and the preferred interactions between different molecules and organic functional groups. Both 2-D and 3-D structure searching are possible with the CSD, in addition to pharmacaphore searching. A PHARMACAPHORE is the specific 3-D arrangement of functional groups within a molecular framework that is necessary to bind to a macromolecule or an active site in an enzyme.
WebCSD, the web portal to the CSD, does not include all the CSD System programs. It does include access to CSD X-Press records that have been automatically processed, but haven't received final curation yet.
A free interactive Teaching Database that is a subset of 500 compounds chosen specifically for teaching purposes is also available.
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:
- Comparative Genomics
- Gene Expression
- Gene Identification and Structure
- Genetic Maps
- Genomic Databases
- Intermolecular Interactions
- Major Sequence Repositories
- Metabolic Pathways and Cellular Regulation
- Mutation Databases
- Protein Databases
- Protein Sequence Motifs
- Proteome Resources
- RNA Sequences
- Retrieval Systems and Database Structure
- Varied Biomedical Content
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.
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.
Abstracting and Indexing Journals and Databases
Specialized A&I services can be found for analytical chemistry, including:
- Analytical Abstracts
- Chromatography Abstracts
- Mass Spectrometry Bulletin (discontinued at the end of 2011)
Several of the A&I services can now be searched as online databases. Analytical Abstracts (Analytical WebBase), produced by the Royal Society of Chemistry, has comprehensive coverage for all aspects of analytical chemistry, including instrumentation and applications. Analytical Abstracts covers more than 100 publications and has included manufacturers' application notes and Australian and British standards, as well as new books.
Analytical Chemistry is concerned with the definitive identification of a substance or the separation of substances from a mixture. The chemical substance that is being analyzed is the analyte, whereas the medium in which it is found is the matrix. As with other sub-disciplines of chemistry, there are specialized reference tools for doing research in analytical chemistry. One particular type of tool that is not found in other sub-disciplines of chemistry is spectral data compilations. Another specialized type of source for analytical chemists is compilations of standard methods.