Chemical Information Sources/Analytical Chemistry Searches

1
Chemical Information Sources/Analytical
Chemistry Searches
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 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
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 Separation
Science
[2]
.
The Encyclopedia of Nuclear Magnetic Resonance (1996-2002) in 9 volumes contains over 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 Encyclopedia of Spectroscopy and
Spectrometry
[3]
(2010). Although the articles are arranged as a traditional encyclopedia in alphabetical order, the
editors provide a separate contents list by topics:
Chemical Information Sources/Analytical Chemistry Searches
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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, among
them:
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 Analytical
Nomenclature (1987).
Treatises
The largest continuing treatise in analytical chemistry is ../Wilson and Wilson's Comprehensive Analytical
Chemistry/. 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.
Standard Methods, Handbooks, and Smaller Works
One of the most popular continuing methods series is Techniques of Chemistry
[4]
(1971-). The early volumes of the
series were issued in a revised edition as Physical Methods of Chemistry
[5]
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:
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
Chemical Information Sources/Analytical Chemistry Searches
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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 the
online version.
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.
Fuel Oil Entry in the ASTM Database
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
[6]
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
[7]
.
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:
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 the
solubility 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 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. Beilstein and Gmelin are available from Elsevier MDL under DiscoveryGate and the
CrossFire 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 to
both experimental and computed data and spectra.
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
Chemical Information Sources/Analytical Chemistry Searches
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Name Wavelengths Transitions
Radio-frequency
10
-1
- 10
3
meters (m)
Molecular rotations, NMR
Microwave 0.1 - 30 centimeters (cm) Molecular rotations, ESR/EPR
Infrared 2.5 - 50 micrometers (m) 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
[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:
Chemical Information Sources/Analytical Chemistry Searches
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Mass Spectrum of Isatin in the Free NIST Chemistry Webbook
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 Spectra Data
[10]
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
[11]
.
A smaller, popular collection of over 240,000 spectra is the NIST/EPA/NIH Mass Spectral Database
[12]
, available
from 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. 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 1.2 million spectra:
All Bio-Rad Sadtler spectra
Chemical Information Sources/Analytical Chemistry Searches
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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 / Universitt 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 by
selected members of the community
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
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:
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 library
service, FTIRsearch.com
[15]
. 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
[16]
. SpecInfo
[17]
is a database of
more than 660,000 proton, C13, MS, and IR spectra that is now available on the Web via Wiley Online Library. Also
available 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 any
of them. Databases such as Chemical Abstracts, Beilstein, or Gmelin may then be of use in identifying a source in
the primary literature. In fact, the CAS Registry database now includes more than 713,000 experimental spectra. In
2009, 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 of
Organic Compounds (Japan), and some are references to spectra in the literature.
Chemical Information Sources/Analytical Chemistry Searches
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Crystallography
The Cambridge Structural Database
[21]
is the largest collection of crystal structure data in the world, with over
500,000 structures. It covers organic and organometallic crystal structures from 1935 onward. 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.
Search Results for Isatin in the Cambridge Structural Database
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 PHARMACAPHORE 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
[22]
.
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
[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 Content
The Protein Data Bank
[24]
and GenBank
[25]
are two of the better known databases for biomolecules. There is a
service from the National Library of Medicine called Entrez
[26]
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
[27]
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.
Chemical Information Sources/Analytical Chemistry Searches
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Another major review serial is Methods of Biochemical Analysis. There are lots of other review serials in the field of
analytical 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 Bulletin
Several 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 of
analytical chemistry, including instrumentation and applications.
Search for Fuel Oil as Matrix in the Analytical Abstracts Database
Analytical Abstracts covers more than 260 journals in 12 languages, manufacturers' application notes, and Australian
and British standards, as well as new books.
Summary
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.
CIIM Link for further study
SIRCh Link for Analytical Chemistry Searches
Problem 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
Chemical Information Sources/Analytical Chemistry Searches
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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
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Article Sources and Contributors
Chemical 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 Contributors
File: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)
License
Creative Commons Attribution-Share Alike 3.0 Unported
//creativecommons.org/licenses/by-sa/3.0/