Chemical Information Sources/Analytical Chemistry Searches 1

Chemical Information Sources/AnalyticalChemistry SearchesIntroduction

Chemists of all types need to be able to identify with certainty the substances they have made, extracted from asource, or sampled in some manner. In some cases, the species they are testing exist for very short periods of time asintermediates in chemical reactions. Whether they are trying to determine the sequences and structure ofbiomolecules with molecular weights in the hundreds of thousands or attempting to detect minute quantities of asmall molecule that is present as a few parts per billion, analytical chemistry provides many tools and techniques tofind 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 asdata compilations that result from newer spectral techniques are all available to assist in the identification of anunknown 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 problemsthe 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 sampleor 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 useof STANDARD METHODS of analysis to ensure that chemists in diverse operating environments obtain the sameresults on the same samples. The methods may involve sampling techniques, sample preparation, methods toseparate or purify a sample, and methods to identify a pure substance or the components of a mixture. Many of thesemethods are gathered in books or series in which are distilled the most reliable and accurate techniques from othertypes of chemical publications. At times it may be necessary for the analytical chemist to create a derivative of theanalyte in order to form a more volatile or more thermally stable substance that can be separated. The technique isparticularly important in chromatography.

Encyclopedias, Dictionaries, Data Compilations, and Treatises

Encyclopedias

The 10-volume Encyclopedia of Analytical Science (2nd ed., 2005) covers three broad areas:•• techniques (e.g., spot tests, mass spectroscopy)•• field or material of application (e.g., forensic science, asbestos)•• analytes (e.g., aluminum, cholesterol, nucleic acids).Other multi-volume works are the Encyclopedia of Analytical Chemistry [1] and the Encyclopedia of SeparationScience [2].The Encyclopedia of Nuclear Magnetic Resonance (1996-2002) in 9 volumes contains over 720 authoritativearticles, the first 200 of which cover the history of this important technique. The encyclopedia appearedapproximately 50 years after the first successful NMR experiments on condensed matter. It covers all aspects ofNMR.Among the more specialized encyclopedias that have recently appeared is the Encyclopedia of Spectroscopy andSpectrometry [3](2010). Although the articles are arranged as a traditional encyclopedia in alphabetical order, theeditors provide a separate contents list by topics:

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•• Atomic Spectroscopy•• Electronic Spectroscopy•• Fundamentals of Spectroscopy•• High Energy Spectroscopy•• Magnetic Resonance•• Mass Spectrometry•• Spatially Resolved Spectroscopic Analysis• Vibrational, Rotational & Raman Spectroscopies.Furthermore, each article is flagged as either a "Theory," "Methods and Instrumentation," or "Applications" article.Seven volumes of the projected 10-volume Encyclopedia of Mass Spectrometry had appeared by the end of 2010.

Dictionaries

A number of one-volume dictionaries appeared in the 1980s for the fields relevant to analytical chemistry, amongthem:• A Dictionary of Spectroscopy (1982)• A Dictionary of Chromatography (1982)• A Dictionary of Electrochemistry (1984)• A Dictionary of Concepts in NMR (1989).The definitive source for nomenclature of analytical chemistry is the IUPAC publication Compendium of AnalyticalNomenclature (1987).

Treatises

The largest continuing treatise in analytical chemistry is ../Wilson and Wilson's Comprehensive AnalyticalChemistry/. It appears that the 2nd edition of another treatise, the Treatise on Analytical Chemistry, (1978-) hasstalled. The 14 volumes of the first part came out between 1978 and 1986.

Standard Methods, Handbooks, and Smaller Works

One of the most popular continuing methods series is Techniques of Chemistry [4] (1971-). The early volumes of theseries were issued in a revised edition as Physical Methods of Chemistry [5] beginning in 1986. Other specializedtitles with important information for analytical chemists who work with biomolecules include Methods of EnzymaticAnalysis in 12 volumes and Methods in Enzymology, a continuing series that now numbers in the hundreds ofvolumes. Included in the latter title are volumes that deal with basic theory, sources of equipment and reagents, andmethods 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 lookfor many of the methods used in testing substances in industry. For example, one finds here a method fordetermining 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 thetypes of information found in the work are:•• Apparutus 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

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•• CAS Registry Numbers where applicable.In addition, the work has an in-depth subject index. It is available in print and online, with continuous revision of theonline version.A much larger work, the Annual Book of ASTM Standards, appears each year with the latest word on how to testvarious materials. It is also good for definitions of certain industrial substances, for example, fuel oil.

Fuel Oil Entry in the ASTM DatabaseThe 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 [6] standards are now on the Web, and a subscription can be placed for as few as 50 copies/year. ASTM alsoproduces the ASTM International Directory of Testing Laboratories [7].Specialized works of this type include Standard Methods for the Examination of Water and Wastewater and theNIOSH Manual of Analytical Methods.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 [8] (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 max from 250-795 nm and thesolubility in water of many stains, dyes, and indicators.

Large Data Compilations

The large data compilations Beilstein Handbook of Organic Chemistry and Gmelin Handbook of Inorganic andOrganometallic Chemistry contain much data of interest to analytical chemists. Now that database versions of theseare available, it is easy to determine if a particular piece of analytical data exists for any of the millions ofcompounds in the databases. Beilstein and Gmelin are available from Elsevier MDL under DiscoveryGate and theCrossFire system, and they can also be found on the systems of somoe of the major vendors. e.g., DIALOG(Beilstein). Similarly, the Registry File in the Chemical Abstracts Service system increasingly provides access toboth experimental and computed data and spectra.

Spectral Compilations

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

Types of Spectra and the Transitions They Engender

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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, theenergy 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 theradiation. The energy is usually represented by the wavelength or frequency. Another method of representing spectrais to record a series of numbers that measure the peaks of the emission or absorption spectra. Either or both methodsmay 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 theradiation source in the far infrared-visible region of the spectrum.Spectroscopy also embraces the technique of mass spectrometry, wherein the instrument measures the distribution ofcharged particles produced after ionization, rather than radiation that is emitted or absorbed. The gas-phase ions areseparated according to their masses or ratios of mass to charge (m/z). The mass spectrometer's beam of high-energyelectrons thus causes organic molecules to ionize and fragment. It then separates the mixture of ions by their m/zratios and records the relative abundance of each ionic fragment. The resultant plot of ion abundance versus m/zresembles spectra produced by other techniques.Mass spectra are among those found in the NIST (National Institute for Standards and Technology) ChemistryWebBook [9], which had in its February 2000 release:•• IR spectra for over 7500 compounds•• Mass spectra for over 10,000 compounds•• UV/Vis spectra for over 400 compounds•• Electronic and vibrational spectra for over 3000 compounds•• Constants of diatomic molecules (spectroscopic data) for over 600 compounds.The Mass Spectrum of Isatin is reproduced below:

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Mass Spectrum of Isatin in the Free NIST Chemistry WebbookIn mass spectrometry, as in other types of spectral depictions, a researcher really needs to know what types ofcompounds or groups yield peaks that match the measured spectrum. Most collections are indexed by the name ofthe compound or by molecular formula. The Important Peak Index of the Registry of Mass Spectral Data lists by m/zvalue the first, second, and third most abundant peaks in the Registry, covering over 50,000 compounds. The WileyRegistry of Mass Spectra Data [10] is the largest commercially available collection of mass spectra. In 2011, Wileyintroduced, in association with emolecules, ChemGate. This web resource, no longer available, enabled a search bystructure of 500,000 compounds to find NMR, IR, or Mass spectra. Wiley bundles NMR spectrum prediction withthe NMR collections (13C, 15N, 17O, 19F, 31P, 1H), based both on algorithm prediction and machine-learningprediction (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 CASRegistry File. The Registry File also has IR absorption spectra from the Japanese Spectral Database for OrganicCompounds [11].A smaller, popular collection of over 240,000 spectra is the NIST/EPA/NIH Mass Spectral Database [12], availablefrom the National Institute for Standards and Technology (NIST).Two companies that have produced a number of standard spectral collections are Bio-Rad [13] and Sigma-Aldrich[14]. Bio-Rad Laboratories encompasses the Sadtler suite of spectra long held by many libraries in printed format. Anoften overlooked place to find your spectrum is the local analytical chemistry laboratory, which likely has some ormany of the large libraries installed on the spectrometers (e.g. Wiley Registry, NIST, Bio-Rad, etc.). Some of theselibraries are quite large.Bio-Rad's KnowItAll Informatics System is an integrated software and database package that provides tools such asdatabase building, management, search, analysis, prediction, structure drawing, and reporting within a single userinterface. Academic institutions may obtain a license for KnowItAll U that includes a collection of software toolsand over 1.2 million spectra:•• All Bio-Rad Sadtler spectra

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•• 390,000 IR, NMR, Raman, and mass spectra (including UV-Vis and additional NMR in Q4)• Most John Wiley & Sons spectra

•• 845,000 IR, NIR, NMR, and mass spectra•• All spectra of Prof. Dr. Wolfgang Robien / Universität Wien

•• 117,000 NMR spectra• SpectraBase™ community database

•• A peer-reviewable database of NMR, IR, UV-Vis, Raman, NIR, and mass spectra edited and reviewed byselected members of the community

•• KnowItAll Informatics System•• KnowItAll AnyWare

•• A web browser-enabled client that is hardware, operating system, and browser independent, allowing access tothe KnowItAll U database collection via Windows, Macintosh, or Linux

The older printed Sadtler collections of Infrared and NMR spectra share a common index that also covers otherprinted compilations such as Varian and JEOL NMR sets. The references to NMR spectra in those sets are indicatedby a "V" and a "J" respectively.Checking the Sadtler Alphabetical Index for isatin, one finds:

Name 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:•• Cumulative Chemical Class Index•• Cumulative Molecular Formula Index•• Cumulative Numerical Index/Cumulative Molecular Weight Index•• Cumulative Spec-Finder Index.Nicolet Instruments Corporation and Galactic Instruments Corporation have developed a pay-per-use spectral libraryservice, FTIRsearch.com [15]. Over 71,000 FTIR and 16,000 Raman spectra are included. Other collections ofelectronic spectra are offered by companies such as Fiveash Data Management [16]. SpecInfo [17] is a database ofmore than 660,000 proton, C13, MS, and IR spectra that is now available on the Web via Wiley Online Library. Alsoavailable are Wiley Registry of Mass Spectral Data [18]. Compound coverage can be verified at Compound Search[19].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 [20] 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 anyof them. Databases such as Chemical Abstracts, Beilstein, or Gmelin may then be of use in identifying a source inthe primary literature. In fact, the CAS Registry database now includes more than 713,000 experimental spectra. In2009, this was comprised of:•• More than 408,000 proton, carbon-13, and heteroatom NMR•• More than 127,000 mass spec•• Nearly 174,000 IR, and•• Nearly 3000 Raman spectra.Some from of these are Wiley, some from BioRad, some from AIST: Integrated Spectral Database System ofOrganic Compounds (Japan), and some are references to spectra in the literature.

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Crystallography

The Cambridge Structural Database [21] is the largest collection of crystal structure data in the world, with over500,000 structures. It covers organic and organometallic crystal structures from 1935 onward. The CSD containsbibliographic 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.

Search Results for Isatin in the Cambridge Structural DatabaseIt has information on the preferred shapes of molecules and the preferred interactions between different moleculesand organic functional groups. Both 2D- and 3D-structure searching is possible with the CSD, in addition topharmacaphore searching. A PHARMACAPHORE is the specific 3D arrangement of functional groups within amolecular framework that is necessary to bind to a macromolecule or an active site in an enzyme.There is also an Inorganic Crystal Structure Database [22].

Biomolecule Sequence and Structure Databases

The last few decades have witnessed an explosion of growth in data files associated with efforts to solve thesequence and structures of proteins, nucleic acids, and other biomolecules. Each year the journal Nucleic AcidsResearch has in the first issue published that year a guide to the databases of interest to molecular biologists [23].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•• Pathology•• Protein Databases•• Protein Sequence Motifs•• Proteome Resources•• RNA Sequences•• Retrieval Systems and Database Structure•• Structure•• Transgenics•• Varied Biomedical ContentThe Protein Data Bank [24] and GenBank [25] are two of the better known databases for biomolecules. There is aservice from the National Library of Medicine called Entrez [26] that links via the Internet the relevant referencesfrom the Medline database to the databases of biomolecular sequences.

The Special Review Issues of Analytical Chemistry [27] and Other Reviews

In alternating years, the American Chemical Society journal Analytical Chemistry published for many years specialissues 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 thermalanalysis, chemical sensors, ion-selective electrodes might be topics found in the latter. These review articlesappeared for at least 50 years.

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Another major review serial is Methods of Biochemical Analysis. There are lots of other review serials in the field ofanalytical chemistry [28].

Abstracting and Indexing Journals and Databases

A large number of specialized A&I services can be found for analytical chemistry, including:•• Analytical Abstracts•• Chromatography Abstracts•• Mass Spectrometry BulletinSeveral of the A&I services can now be had on CD-ROM or searched as online databases. Analytical Abstracts [29]

(Analytical WebBase), produced by the Royal Society of Chemistry, has comprehensive coverage for all aspects ofanalytical chemistry, including instrumentation and applications.

Search for Fuel Oil as Matrix in the Analytical Abstracts DatabaseAnalytical Abstracts covers more than 260 journals in 12 languages, manufacturers' application notes, and Australianand British standards, as well as new books.

Summary

Analytical Chemistry is concerned with the definitive identification of a substance or the separation of substancesfrom a mixture. The chemical substance that is being analyzed is the analyte, whereas the medium in which it isfound is the matrix. As with other sub-disciplines of chemistry, there are specialized reference tools for doingresearch in analytical chemistry. One particular type of tool that is not found in other sub-disciplines of chemistry isspectral data compilations. Another specialized type of source for analytical chemists is compilations of standardmethods.CIIM Link for further studySIRCh Link for Analytical Chemistry SearchesProblem Set on this topic [30]

References[1] http:/ / en. wikipedia. org/ wiki/ Encyclopedia_of_Analytical_Chemistry[2] http:/ / www. elsevierdirect. com/ product. jsp?isbn=9780122267703[3] http:/ / www. elsevierdirect. com/ product. jsp?isbn=9780123744173[4] http:/ / www. indiana. edu/ ~cheminfo/ C471/ tab09-01. html[5] http:/ / www. indiana. edu/ ~cheminfo/ C471/ tab09-02. html[6] http:/ / www. astm. org/ cgi-bin/ SoftCart. exe/ index. shtml?E+ mystore[7] http:/ / www. astm. org/ LABS/ search. html[8] http:/ / www. usp. org/[9] http:/ / webbook. nist. gov/ chemistry/[10] http:/ / www. wileyregistry. com/[11] http:/ / www. aist. go. jp/ RIODB/ SDBS/ cgi-bin/ cre_index. cgi[12] http:/ / www. nist. gov/ srd/ nist1a. cfm[13] http:/ / www. bio-rad. com[14] http:/ / www. sigmaaldrich. com/ Local/ SA_Splash. html[15] http:/ / www. ftirsearch. com/[16] http:/ / www. fdmspectra. com/[17] http:/ / onlinelibrary. wiley. com/ book/ 10. 1002/ 9780471692294[18] http:/ / onlinelibrary. wiley. com/ book/ 10. 1002/ 9780470175217[19] http:/ / www. compoundsearch. com[20] http:/ / bl-libg-doghill. ads. iu. edu/ chem-web/ databases/ crsd/ index. php[21] http:/ / www. ccdc. cam. ac. uk/ products/ csd/[22] http:/ / www. fiz-karlsruhe. de/ icsd. html

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[23] http:/ / www. oxfordjournals. org/ nar/ database/ a/[24] http:/ / www. rcsb. org/ pdb/ Welcome. do;jsessionid=Hj2es+ U65u7-0pr7lZ3umQ**[25] http:/ / www. ncbi. nlm. nih. gov/ Genbank/ GenbankOverview. html[26] http:/ / www. ncbi. nlm. nih. gov/ gquery/ gquery. fcgi[27] http:/ / pubs. acs. org/ journals/ ancham/ index. html[28] http:/ / www. indiana. edu/ ~cheminfo/ C471/ tab09-07. html[29] http:/ / www. rsc. org/ Publishing/ CurrentAwareness/ AA/ index. asp[30] http:/ / www. indiana. edu/ ~cheminfo/ C471/ 471ps6. html

Article Sources and Contributors 10

Article Sources and ContributorsChemical Information Sources/Analytical Chemistry Searches  Source: http://en.wikibooks.org/w/index.php?oldid=2197284  Contributors: Adrignola, Avicennasis, Gary Dorman Wiggins,Jebediabayou, Mb1081

Image Sources, Licenses and ContributorsFile:Isatin ms nist.gif  Source: http://en.wikibooks.org/w/index.php?title=File:Isatin_ms_nist.gif  License: Public Domain  Contributors: NIST (National Institute for Standards and Technology)

LicenseCreative Commons Attribution-Share Alike 3.0 Unported//creativecommons.org/licenses/by-sa/3.0/