Chemical Literature and Scientific Communication

Course #: CH390

AstroChemistry

Why is Chemical Information Important?

  • It is large, diverse and expanding
  • It is complex
  • It is constantly changing
  • It is timeless
  • Can be about making of new substances as well as understanding old ones
  • Chemical Abstracts (from 1907) now has 105 million unique organic and inorganic substances
  • There are specialized chemistry databases, reference books, and websites developed to help you sort through the enourmous storehouse of chemistry information

What is Information?

  • Information is a thermodynamic system as described by Claude Shannon
  • Information is raw data that has been subjected to some treatment (hopefully a catalytic reaction)
  • Information professions try to create organizational strategies to access information more readily

New Information

  • Real learning can make you feel uncomfortable
  • Makes you think that your thinking is deficient
  • If you avoid the confrontation of new information and resort back to a comfort zone, you will lose the opportunity to expand your understanding

Types of Scientific Information/Journals

  • Primary Information: an original publication: journals, patents, thesis, some science books etc.
  • Secondary Information: publication that summaries or condenses primary: reviews, indexes, databases etc.
  • Well known scholarly journals in Chemistry:
    • Nature
    • Science
    • Journal of the American Chemical Society (JACS)
    • Chemical Society Reviews (RSC)
  • For more information see Primary and Secondary Literature in Science

Using Library of Congress (LC) Call Numbers to Find Books in Science

  • Broad Classes: Q = Science, R = Medicine, T = Technology
  • Subclasses: QA = Mathematics, QC = Physics, QD = Chemistry
  • A call number is the location where you find a book on the shelf. eg. Fundamentals of Crystallography has the call number QD 905.2 .F86 2011 (this is the 3rd edition)
  • Laurier Library has call numbers arranged by floors and Q is on the 7th floor
  • Find QD first
  • The next is a number between 1 and 9999
  • Find the number after the decimal
  • Find the next letter and decimal (eg. F86 so F8 or F72 or F855 all come before F86)

Where do I find the ACS style guide in the Library?

  • Located in quick reference 2nd floor and the call number is QD 8.5 .A25 2006
  • Or check it out online here

What is really important to know?

  • attitude and motivation are more important than anything else
  • self-regulation is knowing when to ask for help
  • critical thinking is when you judge information for credibility and integrity
  • metacognition is when you think about how you are thinking, an awareness of the approach you take towards a problem
  • creative thinking is when you come up with new ideas or solutions without any judgement on their merit
  • be honest with yourself and the way you learn
  • physically engage in the classroom; ask questions, make eye-contact, think about how things connect
  • have fun

How to Search?

Astrochemistry Places to Look

Types of Searchers?

  1. Sharpshooter
  • very precise, very specific
  • least amount of patience
  • out quickly

2.Shotgun

  • broad approach
  • bookmark pages
  • take everything

3.Artillery

  • cite first results from search
  • desperate and late
  • lots of information

Searching Google

Developing your Search Strategy

  • Create a research statement using keywords
  • Use keywords and/or controlled language (subject or descriptor or MeSH)
  • Use Boolean operators to connect keywords
  • Search appropriate database and check more than one database
  • Change approaches as necessary, searching is not a linear process but one where you might have to redo searches
  • Keep identifying new keywords and controlled vocabulary to redo searches

Finding Keywords

  • Develop keywords from concepts from your research question
  • Note possible natural vocabulary keywords and synonyms
  • Create concepts into one to three separate terms
  • Do not type in the entire research question into the search box
  • Do not take the first search response (usual sorting is most recent)

Example

  • Search Statement: Identify potential stem cell methodology that could be used for changing valine to glutamic acid in hemoglobin of people with sickle cell disease.
  • Concept 1: sickle cell anemia
  • Concept 2: hemoglobin
  • Concept 3: stem cell methodology
  • Identify Related keywords
  • Concept 1
    • sickle cell disease
    • Hemoglobin S disease
    • globulinopathies
  • Concept 2
    • Beta chain
    • Beta-globin gene
    • codon nucleotide 6
    • Valine
    • Glutamic acid
  • Concept 3
    • Stem cells
    • Gene silencing
    • Gene splicing
    • Gene transfer techniques
    • Targeted gene repair
    • Genetic engineering
    • RNA antisense

Truncation and Wildcards

  • Truncation allows you to search for variant forms for a single search term
  • Wildcards use a symbol to stand in for a set of letters
  • Examples
    • microb* (searches: microbes, microbiology, microbial, microbacteria, microbiologist, microbiologists)
    • bacteri* (searches: bacteria, bacterium, bacterial)
    • behavio*r (searches: behaviour, behavior)
    • gen* (searches: genome, genomics, gene, genotype, genetic, genetics, genera, genus, GenBank, genera)

Boolean Operators

  • OR eg. fruit fly or Drosophila melanogaster
  • AND eg. bird AND song
  • NOT eg. anxiety disorders NOT animal

Things to Remember when dealing with Information

  • Authority is constructed and contextual
  • Information creation is a process
  • Information has value
  • Research as Inquiry
  • Scholarship as a conversation
  • Searching as strategic exploration

Finding Chemical Data Collections

  • ChemSpider: created by Antony Williams but now part of the Royal Society of Chemistry. Includes 32 million (as of Dec. 2014) chemical substances. Searchable for names, formulas, properties & structures.
  • PubChem: from the National Library of Medicine. Contains names, structure, basic physical properties, safety, toxicity, drug and pharmaceutical properties for millions of compounds.
  • CRC Handbook: physical and chemical data arranged into tables. Data on melting point, boiling point, solubility etc. Can also search by substance or property.
  • Merck Index: RS 51.M4 in Quick Reference (main floor of the library). Strongest on data about drugs but also pesticides and other pharmaceuticals. Includes physical data, toxicity, preparation references and uses.
  • SigmaAldrich: Not just a chemical catalogue where you can buy neat stuff. Has CAS registry numbers, molecular formula, links to FT-IR, Raman and proton NMR spectra as well as MSDS.
  • ChemBioFinder: You do have to login but its free. Basic physical data and structural diagrams. Search by name, molecular weight, molecular formula, CAS registry number.
  • Integrated Spectral Data Base for Organic Compounds: From the National Institute of Materials and Chemicals in Japan and contains full spectra. Searchable by compound name, CAS registry number, molecular formula and IR or NMR peaks. Free but don't download more than 50 spectra without permission.
  • NIST Data Gateway: National Institute of Standards and Technology (NIST). IR and mass spectra data as well as UV/visible spectra data.
  • Wolfram Alpha: A computational knowledge engine. It computes answers and provides data.

What to look for in a database?

  • scope: what does it cover?
  • comprehensiveness: how well does it cover the topic?
  • chronological coverage: how many years does it include?
  • access: paper or print? open or not? how do I find it?
  • electronic databases: how easy is it to search? can I do anything 'fancy'? is it a citation database?

What are good databases in Chemistry?

What else is useful?

Structure Drawing Tools
  • ChemSketch: Free downloadable software that lets you draw chemical structures.
  • JME Molecular Editor: Free Java applet which allows you draw molecules and reactions.
  • Marvin Sketch: Free advanced chemical editor for drawing chemical structures, queries and reactions. From ChemAxon.
  • SMILES: a string of letters used as code to describe the structure of a chemical compound.
  • InChI: IUPAC International Chemical Identifier, a mechanism to describe a chemical structure that includes both a human and machine understandable language.

How to read a chemistry paper?

  • check out this video on Youtube

ACS Citation Style

How to Format In-Text Citations

(For more detailed information see ACS Style Guide, pp 287-290.)

Select one of the three methods below to cite in-text references:

Superscript numbers

At the end of the cited information:Fluoridated water as well as various fluoride products such as toothpaste provide fluoride ions necessary for remineralization.┬╣

Within the cited information:Rakita┬╣ states that fluoridated water as well as various fluoride products such as toothpaste provide fluoride ions necessary for remineralization.

Italic numbers

At the end of the cited information:Fluoridated water as well as various fluoride products such as toothpaste provide fluoride ions necessary for remineralization (1).

Within the cited information:Rakita (1) states that fluoridated water as well as various fluoride products such as toothpaste provide fluoride ions necessary for remineralization.

Author name and year of publication

At the end of the cited information:Fluoridated water as well as various fluoride products such as toothpaste provide fluoride ions necessary for remineralization (Rakita, 2004).

Within the cited information:Rakita states that fluoridated water as well as various fluoride products such as toothpaste provide fluoride ions necessary for remineralization (2004).

Note: for two authors use "and": Rakita and Smith. For more than two authors use "et al.": Rakita et al.

How to Format Reference Lists

Books

(ACS Style Guide, pp 300-305)

Single author

Chang, R. General Chemistry: The Essential Concepts, 3rd ed.; McGraw-Hill: Boston, 2003.

Edited Book

Gbalint-Kurti, G. G. Wavepacket Theory of Photodissociation and Reactive Scattering. In Advances in Chemical Physics; Rice, S. A., Ed.; Wiley: New York, 2004; Vol. 128; p 257.

Book in Series

Goh, S. L. Polymer Chemistry in an Undergraduate Curriculum. In Introduction of Macromolecular Science/Polymeric Materials into the Foundational Course in Organic Chemistry; ACS Symposium Series 1151; American Chemical Society: Washington, DC, 2013; pp 113-127.

Article from a reference book

Powder Metallurgy. Kirk-Othmer Encyclopedia of Chemical Technology, 3rd ed.; Wiley: New York, 1982; Vol. 19, pp 28-62.

Articles

(ACS Style Guide, pp. 291-299 and pp. 317-319 for online articles )

Article in a scientific journal

Evans, D. A.; Fitch, D. M.; Smith, T. E.; Cee, V. J. Application of Complex Aldol Reactions to the Total Synthesis of Phorboxazole B. J. Am. Chem. Soc. 2000,122, 10033-10046.

Article in a popular/non-scientific magazine

Manning, R. Super Organics. Wired, May 2004, pp 176-181.

Article from an online journal

Peacock-Lopez, E. Exact Solutions of the Quantum Double Square-Well Potential. Chem. Ed. [Online] 2007, 11, 383-393 http://chemeducator.org/bibs/0011006/11060380lb.htm (accessed Aug 23, 2007).

Theses, Patents, Conferences, Technical Reports

(ACS Style Guide, pp 307-316)

Theses

Thoman, J. W., Jr. Studies of Molecular Deactivation: Surface-Active Free Radicals and S(O)para-difluorobenzene. Ph.D. Dissertation, Massachusetts Institute of Technology, Cambridge, MA, 1987.

or

Gehring, A. PhD. Dissertation, Harvard University, 1998.

Patents Diamond, G.; Murphy, V.; Leclerc, M.; Goh, C.; Hall, K.; LaPointe, A. M.; Boussie, T.; Lund, C. Coordination catalysts. US 20020002257 A1, January 3, 2002.
Conference/Meetings (full-text)

Winstein, S. In University Chemical Education, Proceedings of the International Symposium on University Chemical Education, Frascati (Rome), Italy, October 16-19, 1969; Chisman, D. G.. Ed.; Butterworths: London, 1970.

Conference/Meetings (abstract only)

Kaplan, L.J.; Selder, A. Books of Abstracts, 213th ACS National Meeting, San Francisco, CA, April 13-17, 1997; American Chemical Society: Washington, DC, 1997; CHED-824.

Technical Report or Bulletin

Crampton, S.B.; McAllaster, D. R. Collision and Motional Averaging Effects in Cryogenic Atomic Hydrogen Masers; WMC-AFOSR-002; NTIS: Springfield, VA, 1983.

Web/Online

(ACS Style Guide, pp 316-325)

Note: Different web browsers break the text in different places of a URL. In a printed work, if the URL needs to be broken at the end of a line, the break should be made after a colon or a double slash; before a single slash, a tilde, a period, a comma, a hyphen, an underline, a question mark, a number sign, or a percent symbol; or before or after an equals sign or an ampersand. (CMS 14.2)

Web page National Library of Medicine. Environmental Health and Toxicology: Specialized Information Services. http://sis.nlm.nih.gov/enviro.html (accessed Aug 23, 2004).
Article from an online journal

Peacock-Lopez, E. Exact Solutions of the Quantum Double Square-Well Potential. Chem. Ed. [Online] 2007, 11, 383-393 http://chemeducator.org/bibs/0011006/11060380lb.htm (accessed Aug 23, 2007).

Article from full text database

Begley, S. When Does Your Brain Stop Making New Neurons? Newsweek[Online] July 2, 2007, p 62. Expanded Academic Index. http:/galegroup.com (accessed Aug 23, 2007).

Article published online in advance

Chung, J.M. and Peacock-Lopez, E. Cross-diffusion in the Templator model of chemical self-replication. Phys. Lett. A [Online early access]. DOI:10.1016/j.physleta.2007.04.114. Published Online: June 12, 2007. http://www.sciencedirect.com (accessed Aug 23, 2007).

Computer Program

SciFinder Scholar, version 2007; Chemical Abstracts Service: Columbus, OH, 2007; RN 58-08-2 (accessed Aug 23, 2007).

Citation Tools

Making a Poster

Examples

http://scienceintheclassroom.org/research-papers/chemical-reactions-clos...

http://pubs.acs.org/doi/abs/10.1021/jf505075n

http://cen.acs.org/articles/86/i25/Understanding-Healthier-Foods-Analyti...

http://careers.queensu.ca/sites/webpublish.queensu.ca.cswww/files/files/...

Peer Review

Make peer Review Scientific from Nature: http://www.nature.com/news/let-s-make-peer-review-scientific-1.20194

In Referees we Trust from Physics Today: http://physicstoday.scitation.org/doi/full/10.1063/PT.3.3463

Copyright Transfer Agreements

JAMA agreement: http://jama.jamanetwork.com/data/ifora-forms/jama/auinst_crit.pdf

Wiley-Blackwell agreement: http://media.wiley.com/assets/1540/86/ctaaglobal.pdf

CC-Licences

http://www.teachthought.com/the-future-of-learning/technology/the-ultima...