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Organic Chemistry: Primary Literature - Journal Articles

Finding Journal Articles for Organic Chemistry

Where to search for articles on organic chemistry topics may depend on what you're trying to search. If you want to start with a compound or reaction, you may want to start with SciFinder-n or Reaxys. Both allow you to start with an compound, view associated properties (with literature references), and then retrieve reactions involving that compound and filter those results to view the reactions and literature references of interest. You can also start with a reaction (drawn or imported from ChemDraw) and search on the reaction. SciFinder-n does require a one-time registration (must be on campus network, including protected wifi or VPN, to access this page).

You can also use SciFinder-n and Reaxys for topic/keyword searching, as well as Web of Science, Google Scholar, PubMed and other databases.

More About SciFinder-n

SciFinder-n is a collection of chemical databases, including: 

  • CAS Registry - Database of 204 million organic and inorganic substances, with structures, names, synonyms, CAS Registry numbers, calculated and experimental properties, and spectra.
  • CAPLUS - Comprehensive index of the chemical literature, from 1907 to date with some selective earlier coverage. More than 52 million records, including journal articles, patents, conference proceedings, meeting abstracts, technical reports, and more.
  • CASREACT - Millions of single- and multi-step reactions, including synthetic preparations, from 1840 to present. Now with a retrosynthetic planner.
  • CHEMCATS - Access to chemical supplier catalogs, including pricing and availability.

You can search SciFinder-n by research topic, as well as by substance or reaction. For best results, search Reaxys and SciFinder.

SciFinder-n is restricted to current UC San Diego faculty, staff, postdocs, and students

SciFinder-n does requires a user registration. If you don't already have a SciFinder or SciFinder-n account at UC San Diego, go to the SciFinder-n at UC page and follow the instructions to register. VPN must be enabled for you to get to the registration information. Use your ucsd.edu email address. Once registered, you will still need to run VPN when searching SciFinder-n from off campus 

Use of SciFinder-n is for educational and academic research purposes only.

There is no visitor access for SciFinder-n in the Library.

Release notes for SciFinder-n.

New Features 


CAS Formulus - Curated formulations from journals, patents, and product inserts. Search by formulations or ingredients 

CAS Analytical Methods - Browse, search and compare analytical methods, including materials, techniques, and equipment.

Retrosynthesis Planner: Generate a full retrosynthetic analysis of all known synthetic routes for a given molecule; organize into easy to navigate synthetic plans; and access commercial source availability and pricing.

PatentPak: Full-text searching of 18 million patents, with chemical substances marked so they can be easily found within the patent.

ChemDoodle: Touch-friendly structure editor for drawing on phones and tablets. Structures drawn in ChemDoodle will be the same in CAS Draw, and vice versa.

Additional Enhancements

  • Monthly release schedule for feature enhancements.
  • More options to filter reference, substance, and reaction results.
  • “Search All” to search across the substance, reaction, and references databases.
  • Familiar searching options: booleans, truncation/wildcards, parentheses, e.g. (flavor OR odor) AND menthol.
  • Combined keyword and structure searching.
  • An option to exclude particular results from searches.
  • Autosuggesting search terms.
  • Relevancy-based sorting of results now the default.
  • Reaction search results grouped by scheme (same reactants and products).
  • Live History – edit and rerun past searches.
  • Clearer labeling to connect you to full-text articles, now with UC-eLinks included in the options.
  • Citation mapping to quickly see cited and citing articles.
  • Improvements in combined search functionality: two authors, author(s)/journal, author(s)/organization, two substance property data points.
  • Easy to keep up with new releases of SciFinder-n and get help from the account page.
  • Automatic deduping of CAS/Medline records (coming later this summer).
  • Ability to have multiple tabs running without getting kicked out of sessions.

From the SciFinder-n record, whether from the full record or results list, click the Full Text button under the abstract.

The DOI will take you to the publisher's website where the article is available, and in most cases this is all you need to do to get the article (but make sure that VPN is running if you're off campus).  

You can also use the Get It At UC option as well to go to the full text. The advantages of using Get It At UC: 

  • Links to the full text article if we have access from somewhere other than the original publisher, like the pre-1997 Science articles on JSTOR
  • Connect you to interlibrary loan to request article through interlibrary loan if we don't have it.

You can search for substances in SciFinder-n by

  • Name and/or CAS Registry Number, using the Substances search
  • Molecular Formula
  • Structure or Substructure. SciFinder has its own structure editor, but you import .mol files or draw your structure in ChemDraw and launch SciFinder from there.

From the CAS Registry record, view:

  • Other names and identifiers
  • Data
    • Experimental property data, with associated article references in SciFinder.
    • Experimental spectra, either actual spectra from companies like Bio-Rad, or references to articles.
    • Predicted properties and spectra
  • Regulatory information

And get links to retrieve:

  • References to journal articles, patents and other documents, limited by subcategories (crystal structure, preparation, analytical study, etc).
  • Commercial suppliers for the substance.
  • Reactions, limited by one or more roles (product, reagent, etc.)

Reaction searching can be done in SciFinder-n by:

  • From a substance record, go to Reactions, and select which role(s) for your substance from the filters to the left.
  • Use the structure editor to draw the reaction, import the reaction structures from ChemDraw, or launch the SciFinder search from ChemDraw. You can run the search on the structures exactly as drawn or broaden to a substructure search.

Reactions can also be searched as a research topic, which will give you references as results, rather than reactions.

Reaction results can be filtered by reaction details (reagent, solvent, catalyst, yield, steps, reaction classification, non-participating functional groups) or publication details like journal title and publication year.

Each reaction includes reaction details (reagents, solvents, steps/stages, etc.) and a link to the associated reference to a journal article, patent, or other source. Click on View Reaction Detail for more information about the reaction from MethodsNow. For drawn reactions, you may be able to filter by similarity.

With the Retrosynthesis Planer, generate a full retrosynthetic analysis of all known synthetic routes for a given molecule; organize into easy to navigate synthetic plans; and access commercial source availability and pricing.

Along with the built-in help menu within SciFindern, CAS also provides a set of training materials on their SciFinder-n support page. You can also view previous webinars and register for upcoming webinars.


Contact Teri Vogel (tmvogel@ucsd.edu) if you have questions about using SciFinder, or want to set up a training consultation.

More About Reaxys

Reaxys is a database for the chemical literature, with millions of:

  • indexed journal article and patent references
  • organic, inorganic, and organometallic, with 500+ property data fields
  • chemical reactions

Every reaction and every property data point has at least one associated journal or patent reference.

Reaxys indexes the journal literature further back than SciFinder-n, and indexes deeper into the articles for property data. Like SciFinder-n, Reaxys can be searched by topic/keyword, as well as by substances and reactions. Reaxys also has a query builder to create combined searches (e.g. substances with a certain refractive index, a melting point range, and available IR spectra). For best results, search Reaxys and SciFinder-n.

Off-campus access to Reaxys is restricted to current UC San Diego faculty, students and staff. You must be logged into the VPN client, but you do not need to create an additional individual account unless you want to set up search alerts.

Visitors can access Reaxys from the Library computer stations.

You can search for substances in Reaxys by

  • Name
  • CAS-Registry Number
  • Molecular Formula
  • Structure or Substructure, via the structure editor. You can also import from ChemDraw or launch a Reaxys search from ChemDraw.
  • One or more properties, using the Query Builder to drop and drag fields for various properties, then add enter numbers (or ranges, < and >).

From the Reaxys record, view:

  • Physical Data
    • Data broken out by a few common properties (e.g. melting point, density), and the rest alphabetically. Each data point has at least one literature reference.
  • Spectra
    • Broken out by types of spectra. No spectra are included, but each reference gives a description of what will be found in the article, like chemical shifts or an actual spectrum. 
  • Ecotoxicology 
  • Other data, including isolation from natural products.

And get links to retrieve:

  • References to journal articles and patents
  • Reactions, and specifically Preparations.
  • Commercial suppliers for the substance

 

Reaction searching can be done in Reaxys by:

  • Topic search (e.g. synthesis of caffeine), which should map to reaction results.
  • From a substance record, link out to Preparations or Reactions.
  • Use the structure editor to draw the reaction, import the reaction structures from ChemDraw, or launch the SciFinder search from ChemDraw. You can run the search on the structures exactly as drawn or broaden to a substructure search.

Reaction results can be filtered by reaction details (reagent, solvent, catalyst, yield, steps, reaction classes, commercial availability) or publication details like journal title and publication year.

Each reaction includes some reaction conditions (reagents, solvents, steps/stages, etc.), a link to at least one associated reference to a journal article or patent, and a link to find similar reactions. Some reactions also include more detailed experimental procedures.

 

The Retrosynthesis Planner does just that: helps you to create synthesis plans for substances in the Reaxys reactions database. For more information on how the Synthesis Planner works, consult this step-by-step tutorial and video.

Reaxys has provided a series of workflow-based tutorials and video tutorials.


Contact Teri Vogel (tmvogel@ucsd.edu) if you have questions about using Reaxys, or want to set up a training consultation.