Overview

• Chemical literature

-Introduction
-Types of article
-Handbooks

• Searching the chemical literature

-Introduction
-Chemical Abstracts - Scifinder Scholar
-Beilstein
-Science Citation Index – Web of Knowledge
 Literature 1 - Purpose

• The sharing of knowledge

-Years ago (before 1800) scientific results were kept a secret.

-In the middle of the eighteen hundreds the first scientific journals were
started in Germany, France and England.
-Today the sharing of knowledge among specialists, is a foundation stone of
research.

• “Two hours in the library saves you months in the lab.”

-It is not scientific, not practical and just plain stupid not to investigate the
literature before you start a research project.
-You risk doing a lot of work only to find out later that other people have
already described this in the literature.

• There are several hundred journals within chemistry alone.

-Organic chemistry has been around for More than 150 years with as we
know it today.
-Millions of pages are published in journals every year
-There are also patents and lots of other published work such as textbooks
-How are we to navigate through all of this?
 Literature 2 – Types of publications
• Primary literature (new results).
-Research papers, In journals, peer-reviewed, new results.

• Communications (letters)
-Interim results.
-Often a full paper is published later.
• Full papers/articles.
-More thorough investigation than communications.

-Patents
• New results, the same as research papers.
• For the protection of copyrights.
• N.B. not peer-reviewed.
-Dissertations (masters, Ph.D., thesis).
-Lectures/posters at conferences.

• Secondary literature
-Reviews (in journals, peer-reviewed).
• Fast introduction to a new topic, often up-to-date.
-Monographs/handbooks
• Book/series of books/encyclopedias on a single topic
• Often older information.
• Handbook with a collection of experimental procedures, good for standard
reactions.
 Literature 3 – Chemical handbooks

• CRC Handbook of Chemistry and Physics

-Good source of information for physical chemistry
• Vogel’s Textbook of Practical Organic Chemistry
-Gives descriptions of chemical reactions and reagents.
• Fieser and Fieser’s Reagents for Organic Chemistry
-Description on how to make common reagents.
• Purification of Organic Laboratory Chemicals
-How to purify common organic compounds.
• Aldrich and Lancaster chemical catalogue
-Has density, boiling point, melting point molecular weight.
-Aldrich has separate reference book for spectra on (NMR, IR)
-Lancaster has some references literature to show how the chemical can be used.
• Organic Syntheses
-Has information on many typical reactions.
-Organic Syntheses is online at http://www.orgsyn.org
 Literature 4 – Journals
• Publishing House
-A publisher issues many journals with different topics.
-American Chemical Society (ACS), Royal Society of Chemistry (RSC), Wiley and Elsevier.
-Almost all are in English, older chemical literature is often in German or French.
• Journals
-Different quality (cutting edge science or “boring” results).
-Different impact factor (how many people read and refer to articles in the journal).
-Different contents (topics and kind of articles).

• Printed editions in the library of the biggest/most important chemical journals.

-Printed editions are expensive to buy and to store. Therefore only until 2002.
• Since 1995 (almost) everything is online as PDF-files
-Some publishers even have PDF-files of their entire archives (ACS).
-Search either www.statsbiblioteket.dk or the list from our library’s website
(www.chem.au.dk)
-Online access from Kemisk Institut or the Statsbiblioteket with a login (library ticket).
• Copies of articles in journals that cannot be found online or in the library can be ordered by
the librarian or by the Statsbiblioteket
-Takes around a week.
-Might cost money
-Typically it will not be necessary for Kemi23
 Literature 5 – The road to a publication
• Simplified process from idea to publication
-Idea for a project.
-Literature search (must also be done continuously).
-Experimental work.
-The manuscript/paper is written.
-Submitted to a publishing house.
-Editor sends the manuscript to expert reviewers in that area (peer-review).
-Reviewers comment on the manuscript and indicate whether it should be accepted for
publication.
-The manuscript is changed according to their suggestions. Perhaps additional
experiments are needed.
-The corrected manuscript is send out.
-The article is published, often first on the net as PDF-file and then in printed edition.

• Peer-review maintains a high scientific standard

-Impartial experts (as reviewers) check the manuscript for errors etc.
-The identity of the reviewer is secret.
-Cutting edge research can be published in the best journals (JACS and Angewante).
-Good, but not as exciting results go to journals of lower standard.
-Insufficient, faulty or very bad results cannot be published and are neglected.
 Literature 6 – Full papers
• Bibliography information
-Periodical name, year, volume, page
-Title,
-Author
List of students who did the work either in order of who did the most work or
alphabetical.
Corresponding author (usually the professor) his name is marked with a star
-Date received, date accepted
• Abstract
-Short summary on the nature of the work.
• Introduction
-Gives the background information for the paper including previous work done and why
the research has been carried out.
• Results
-List of the results obtained in experiments
• Discussion
-Discussion of what the results mean and maybe a theory to explain them.
• Conclusion
-Short conclusion summarising the important points of the paper.
• Experimental section
-Experimental procedures and characterisation of compounds
-References/notes
-List of information used, either in footnotes or at end of paper.
• Supporting information
-PDF file of NMR spectra or crystallographic information.
Literature 7 – Full paper
 Literature 8 – Communications
• Communications are much shorter than full papers.
-They are often only 2 pages long although in some journals they can be up to
five pages.
-It is common for a communication to be published first to claim an area for
yourself and then for a full paper to follow.
-Supporting information is generally not included in the paper but in
supplementary information.
 Literature 9 – Kemitidsskrifter
• Some journals are better than others!

• Nature and Science are the best (not easy to get organic chemistry in here!)

• Reviews subjects within chemistry

-Chemical Reviews (Chem. Rev.)
-Chemical Society Reviews (Chem. Soc. Rev.)
-Accounts of Chemical Research (Acc. Chem. Res.)

• The best journals for organic chemistry

-Journal of American Chemical Society (J. Am. Chem. Soc. – JACS)
-Angewante Chemie (Angew. Chem. – Angewante)
-Journal of Organic Chemistry (J.Org.Chem – JOC)
-Chemistry – A European Journal (Chem.Eur. J.)
-European Journal of Organic Chemistry (Eur. J. Org. Chem.)
-Chemical Communications (Chem. Commun. – ChemComm)
-Tetrahedron (Tetrahedron)
-Tetrahedron Letters (Tetrahedron Lett. – Tetlett/TL)
-Organic Letters (Org. Lett.)
-Organic and Bioorganic Chemistry (Org. Bioorg. Chem.)
• New, J. Chem. Soc. Perkin Trans. 1 and J. Chem. Soc. Perkin
Trans. 2. combined
 Literature 10 - Referencer
• In scientific literature (and others) all references used must be given. Otherwise
you are guilty of plagiarism.

• Two different styles of writing references.

-American (ACS – American Chemical Society)

• Katsuki, K; Sharpless, K.B; J.Am.Chem.Soc., 1980, 102, 5974

Surname, Initial; journal abbreviation, year (bold), volume (italics),
page number.

-European (RSC – Royal Society of Chemistry (British))

• G. Pattenden and G.M. Robertson, Tetrahedron Lett., 1986, 27, 399

Initial. Surname, journal abbreviation (italics), year, volume (bold),
page number.

-It is important to choose one style and keep the style consistent when writing
your references..
 Literature searching 1 - Problem
• There are millions of articles, books and other sources of information about
chemistry

• How do you find the information you require?

-You are searching for a needle in a haystack.

• In the old days:

-Large collections of books were used.
-Indexes could be searched by hand for compound names or subject.
-This was very slow and difficult to search through.
-Reference books were only updated every year or less.

• Now: we have online databases

-Books are almost obsolete!
-Incredible tool, has revolutionised the way we search for literature.
• Can search for reaction type or structures
• Find articles online in PDF format.
-Most are online here in the department.
 Information retrieval 2 – Chemical Abstracts

• Chemical Abstracts
-Huge database with abstracts from pretty much all chemical publications
(articles, patents and others).
-All compounds have an unique CAS Registry Number.
-Used to be indexed in books – now it’s online.

• Online database – Scifinder Scholar

-CAS Registry (1957-) >24 million org/inorg. compounds.
-References (1907-) >23 million articles, patents (contains abstracts).
->9.000 journals indexed.
-Updates daily, >400 new compounds, >3000 new references.
-Reactions (1840-) >8 million reactions.
-Also has an index of >800 chemical catalogues.
-Also can search in the pubmed-database (life sciences).
 Information retrieval 3 – Scifinder Scholar
• Advantages
-Access to the entire Chemical Abstracts database.
-Biggest chemical database. Contains by far the most journals and patents.
-Updates daily.
-Search for keywords in abstract/keywords, structures, publishers and
additional bibliographic information.
-Shows abstract from the article, references in the article and references to
the article (citations).
-Many possibilities to search and choose from in the hits.
• e.g. only reviews, only newer than 2001 etc.
-Many possibilities to help sort out and analyze hits.
-ChemPort to online articles, many articles can be found easily and quickly
without having to go to the library or the publishers homepage.

• Disadvantages
-Unfortunately only one user at a time for the entire chemistry department as
licenses are so expensive.
• REMEMBER TO LOG OUT AFTER USE!
• Easiest access in the late afternoon/evening.
 Information Retrieval 4 – Beilstein

• Old German database for chemical searches

-Has existed since 1881.

-Can search for structures, reactions and chemical information (such as melting
point, boiling point and density).

-Access Beilstein through Crossfire server.

-Crossfire also lets you use Gmelin (inorganic chemistry).

• Beilstein database

-Organic reactions and structures (1771-Present) >8 million structures and >10
million reactions.

-Can access physical, chemical and biological properties. >20 million. Properties.

->175 periodical indexes.

-Updates every 3 days.

 Literature search 5 – Crossfire Beilstein

• Advantages

-Centred around organic chemistry.

-Easy to search for structures as well as substructures.
-Can also search for specific reactions.
-Also shows physical and chemical properties with literature references for
NMR data and experimental procedures.
-Possible to search for distinct catalysts or solvents for more specific
searches.
-Can find required article with one click using the literature link.

• Disadvantages

-No abstracts from before 1980

-The literature link often does not work even though the article is available
online.
-The database does not include all journals so you can’t rely on the results as
being comprehensive.
 Literature seach 6 – Web of Knowledge

• Science Citation Index

-Database of publications and references
-Lots of access, www.isiknowledge.com (unlike scifinder)
-Also contains
• Impact Factors
-How ”good” is a journal
• Advantages
-Often updated
-Has more than only science
-Can search for key words in abstract, authors or document
-Shows abstract of article and references
-Can also check new articles which cite the article you are interested in.
-Easy to get the full text of articles

• Disadvantages
-No articles before 1945.
-Can not search using structures only text.
 Literature searching 7 - Diverse
• Other online databases:

-SDBS – spectra (including NMR) of many simple compounds.

-KIROS – Chemistry departments chemical register and safety data.
-Pubmed – life science (biochemistry, microbiology and medicine)
http://www.pubmed.org
-Broomhilda – list of books in the chemistry department library.
-Google scholar: ok for general or quick searches

• When you look for experimental procedures:

-Start out with Beilstein which is often the easiest.

-Always find more than one – preferable 3-4 different methods. Compare and
choose the best (easy, safe, fast, cheap, high yield and purity).
-Don’t underestimate the usefulness of looking in books instead of searching
for articles.
-Check references carefully when a relevant article is found.
-Get the procedure approved by the instructor before you start the syntheses.