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CHEM 3358: Advanced Chemical Synthesis Lab

ChemDraw

  • Link to download ChemDraw is in CLIO (on library computers, go to Scientific apps - ChemDraw Professional 17.0)
  • The first step is to draw bonds without the letters - make sure the lines touch at the vertices.
  • Then add the atoms at the vertices using the letter tool. The default is C.
  • Example:

  • To make it look more regular, select the lasso or marquee tool and click on the structure, then click on Structure – Clean up structure
  • To find the name for the structure, go to Structure – Convert structure to name
  • Various windows, (e.g. Analysis) are under the View menu item.
  • To export to SciFinder, save the molecule in .mol file type
  • You can now also directly search Scifinder from Chemdraw (under the Search menu item).
  • Columbia Libraries ChemDraw tutorial and information about downloading the Activation Code.

 

SciFinder

Getting Started

Structure searching

  • Click on Chemical Structure on left to draw a structure.
  • You can import a structure from ChemDraw - the Import symbol is at the top left.
  • To find information about the structure, click on Exact search or Substructure search on right.
  • Then you can select one of the structures found, and click on Get References to find articles about it.
  • You can also look at Experimental Properties and Experimental Spectra.

Research Topic Searching

  • Example: oxidation of olefins with hydrogen peroxide
  • SciFinder automatically searches related terms and substance names.  It also considers alternate spellings and word endings.  Boolean operators are not used and there are no truncation symbols, or proximity operators.
  • When looking at item record, click on Link to Other Sources to find the full text.
  • You can also find properties and spectra of chemicals mentioned in the article.

 

Hands-On Exercises

1. Draw this structure in Scifinder:

  • Do an Exact Structure search and find its CAS number.
  • Find the references for that substance; how many articles are there that have info about its preparation?
  • Find the NMR and optical rotation data for this substance.

 

2. Searching for a research topic in Scifinder and exporting references to EndNote:

  • Open EndNote, if not already open.
  • In Scifinder, search for iodobenzene diacetate
  • Click on Get references and sort by Citing References
  • Export the two most highly cited references to EndNote.

 

Google Scholar

Pros of scholar.google.com:

  • You can copy and paste the title of an article and quickly get to the full text.
  • You can enable e-Link so that you can access the Columbia subscriptions to full-text materials, even when you're off-campus (go to Settings - Library links).
  • You can import directly into EndNote

Cons of scholar.google.com:

  • No subject headings or other added metadata
  • You have to search full text or allintitle:
  • You can only sort by relevance or date

 

Web of Science

  • Use CLIO to access Web of Science – all databases
  • Example: oxidation of olefins with hydrogen peroxide
  • Sort results by times cited
  • Generate a Citation report.

 

WebCSD: Cambridge Structural Database

  • Use CLIO to access the Cambridge Structural Database, from the Cambridge Crystallographic Data Centre
  • You can search for structures and articles in various ways, e.g. compound name, DOI, author, etc.
  • 3D view of structures is available when you do a search
  • Example: octadecadiene
  • Example: c.m. rojas as author

 

EndNote and Mendeley

EndNote

  • Barnard Library EndNote Guide
  • There is a Desktop version and a Web version, and you can sync your references between the two
  • On library computers, to start collecting references, go to File - New... and save your new library with a name you choose, or use "My EndNote Library.enl"
  • You can attach a pdf to a reference
  • To enter a new reference go to Collect - New Reference (Web version) or References - New Reference (desktop)
  • CSE Style is not one of the styles provided by EndNote, so if you want to use CSE, use APA style and correct the references in the bibliography:
    • Remove periods after authors’ first name initials
    • un-italicize the journal titles
    • remove parentheses from the year
  • Guide to Scientific Style and Format

Mendeley

  • There is a Desktop version and a Web version, and you can sync your references between the two
  • Download the Mendeley extensions for your browser.
  • You can drag and drop a pdf into Mendeley, and it will find the metadata for you.