CHEM 400 Chemical Literature A short course in the chemical literature, ethics and chemical careers. Dr. Michael W. Justik Penn State Erie, The Behrend College Fall 2016

Chemical Literature Why a course in chemical literature? Huge: Chemical Abstracts:Indexes 9,000 journals currently 40,000 journals since ,993,118 abstracts (865,066 last year) 26,623,929 substances Beilstein: 9,271,617 organic compounds 9,726,867 reactions Gmelin: 2,219,064 inorganic and organometallic 1,718,428 million reactions 84.5% English

Chemical Abstracts Since 1907

Why a course in chemical literature? Complex: Overlaps with physics, biology, medicine, pharmaceuticals, geology, materials, forensics… Not just keyword searches.numerical data chemical formula structural features Chemical nomenclature Chemical Literature

Why a course in chemical literature? Search Tools Evolving Rapidly: Google Web of Science STN SciFinder Scholar MDL CrossFire Commander Web: Beilstein and Gmelin Online: Chemical Abstracts Online Science Citation Online: Chemical Literature

Types of Scientific Literature Primary Journals Peer reviewed Not magazines Conference Proceedings Usually reviewed by a single editor Lectures presented at conferences in book form Dissertations (Ph D), Theses (Masters), Grant Reports Not as easy to find

Types of Scientific Literature Secondary Treatises Muli-volume on a single subject. Comprehensive Detailed bibliography over a long period Multigraphs and Monographs Usually smaller then a Treatise Multiple or single authored book on one topic Encyclopedias and Dictionaries Broad and not detailed

Types of Scientific Literature Secondary Reviews Review articles, narrowly defined Extensive bibliography Indexing and Abstract Journals Up-to-date, published frequently Chemical Abstracts, Science Citation, Beilstein

Types of Scientific Literature Tertiary Guides to Literature References to references Computerized Search Engines Beilstein Electronic Chemical Abstracts, Science Citation,

Primary Literature Publication: the making public of information, by whatever means - oral, printed or electronic. Publication has become a means not only for disseminating information, but also a tool for evaluating a scholar's performance: "Publish or perish."

Scientific Journals Journals vary widely in specialization: Very broad, covering all of science (more or less...). Nature Science

Journals vary widely in specialization: Covering all of a major section of science, such as chemistry, biology or geology. Journal of the American Chemical Society Physical Review Letters Angewandte Chemie Scientific Journals

Journals vary widely in specialization: Covering a major subsection of science, such as organic chemistry or solid state physics. Journal of Organic Chemistry Inorganic Chemistry Dalton Transactions Scientific Journals

Journals vary widely in specialization: Covering a highly specialized area of research. Biogeochemistry Nano Letters Crystal Growth and Design Scientific Journals

Journals vary widely in types of articles: Major reviews: Longer articles summarizing research in a particular field, usually over a specified chronological range. Generally written by scientists who are expert in the field. Accounts of Chemical Research Chemical Society Reviews Chemical Reviews Scientific Journals

Journals vary widely in types of articles: Major original papers: The majority of scholarly journals carry full-length articles on original research. Perkin Transactions Tetrahedron Scientific Journals

Journals vary widely in types of articles: Brief communications: Some journals specialize in rapid publication of short announcements of research results. Organic Letters Chemical Communications Scientific Journals

Structure of a Journal Article Main purpose of a scientific paper: report new results, and to relate these results to previous knowledge in the field. Most scientific papers follow a standard format. They are divided into several sections with each section serving a specific purpose. The exact format may vary slightly. Only full articles contain all these sections. Letters and communications are shorter, containing a brief introduction, combined results/discussion and no experimental.

Bibliographic information Article title, authors, author addresses and Structure of a Journal Article

Abstract or Summary Usually at the beginning, although may not be given this title. This short section serves as a summary of the paper. Generally, it gives a brief background to the topic; describes concisely the major findings of the paper; and relates these to other work. This logical order is also that of the paper as a whole. Structure of a Journal Article

Introduction Not always with that title. Gives background knowledge needed for reader to understand why the findings of the paper are important. Typically describe the state of knowledge in the area; then focuses on the particular aspect that led directly to the work described. In many papers, major conclusions of the paper are presented at the end of this section, so that the reader knows the major answers to the questions just posed. Structure of a Journal Article

Experimental Sometimes called Materials and Methods. In some journals this section is the last one and in others it comes after the Introduction. Describes the materials used in the experiments, and the methods by which the experiments were carried out. In principle, this description should be detailed enough to allow other researchers to replicate the work. In practice, these descriptions are often highly compressed and they often refer back to previous papers by the authors. Structure of a Journal Article

Results Describes the experiments and the reasons they were done. Generally, the logic of the Results section follows directly from that of the Introduction. The Introduction poses the questions addressed in the early part of Results. Beyond this point, the organization of Results differs from one paper to another. In some papers, the results are presented without extensive discussion, which is reserved for the following section. Structure of a Journal Article

Discussion Several purposes. First, the data are interpreted or analyzed to show what the authors believe the data show. Any limitations to the interpretations should be acknowledged, and fact should clearly be separated from speculation. Second, the findings of the paper are related to other findings in the field. This serves to show how the findings contribute to knowledge, or correct the errors of previous work. Often combined with Results. Structure of a Journal Article

Conclusion Sometime (but not always) an article may contain a Conclusion paragraph summarizing and reiterating the main points from the Results and Discussion. Sometime a conclusion paragraph may appear at the end of the Discussion. Structure of a Journal Article

Acknowledgements The section in which various contributions of other workers (not listed as authors) are recognized and any funding sources. Structure of a Journal Article

References A list giving references to papers and other works cited in the text. May come at the bottom of each column (as footnotes) or a separate section at the end. Typically, the citation is given as a superscript. Structure of a Journal Article

Veliz, E. A.; Easterwood, L. M.; Beal, P. A. J. Am. Chem. Soc. 2003, 125, ACS Style Guide Page 215 Abbreviations of most cited journals. journal abbrev.yearvolumepage numbers (inclusive) Last name, initials separation Structure of a Reference

Figures, Tables and Schemes Papers usually contain Figures, Tables and Schemes. These contain data described in the paper. The figures and tables also have legends, whose purpose is to give details of the particular experiment or experiments shown there. Look for numbering schemes throughout the text, particularly in synthesis articles. Structure of a Journal Article

The article may have supplementary or supporting information. For print journals, this usually comes on microfiche; electronic journals may have links to the material online. The precise structure required will vary somewhat from journal to journal; nearly all have an "Instructions to Authors" section. Structure of a Journal Article

Peer Review The majority of scientific journals publish peer-reviewed articles, also called refereed articles. In these journals, the editor sends submitted articles out to persons expert in the field of the article. The referee comments on the article and the research it presents. The editor then decides whether to accept the article as is, send it back to the author for revision, or reject it outright. Reviewing helps uphold scientific standards, but it adds to the delay between research and publication - often a year between submission and publication.

Although it is tempting to read the paper straight through as one would most text, it is more efficient to organize the way one reads. Generally, one first reads the Abstract in order to understand the major points of the work. Reading a Scientific Paper

One extremely useful habit in reading a paper is to read the Title, Abstract and Introduction and before going on, review in one's mind what one knows about the topics and concepts discussed. If there are things you are unfamiliar with you may need to do some background reading. Often the Introduction will contain many references, some of which may help, but you may find yourself in need of more general information. For more general background go to the secondary source of literature we have discussed in class (books, encyclopedias etc.). Reading a Scientific Paper

Once you have gained any background you may need, it is time to tackle the Results and Discussion. As you are reading, ask yourself the following questions: Check the Conclusion briefly to see where it is going. Reading a Scientific Paper

1.What is the main point of the paper? What scientific issue is the author addressing? What questions are the author asking? What is the purpose of this research? Reading a Scientific Paper

2.What work has been done previously on this topic? How does the author’s questions/purpose fit into this context? How does it fit into the “big picture”? Reading a Scientific Paper

3.How does the author propose to answer these questions? What techniques or methods does the author use to address these questions? How will these techniques or methods lead to the answer? Reading a Scientific Paper

4.What were the results for the experiments? What did the author observe when the experiments were run? Reading a Scientific Paper

5.What did the author conclude from these results? Were the results justified? Did they give the results the author was seeking or expected? Did they answer his question? Reading a Scientific Paper

6.Did the results lead the author to suggest further or different experiments to be done?

A Final Thought You are not obliged to accept the paper as fact. However, rejecting it requires sufficient background and fundamental knowledge of the subject that is acquired by reading the literature and/or contributing to it.