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Chemistry

A guide to chemistry resources and the A.D. Allen Chemistry Library.

Frequently Asked Questions

On this page, you will find answers to common chemistry- and research-related questions.

What is...
Common terms used in chemistry databases and research.
 

How do I find information on...
Need help starting patent research or finding solubilities? Check for an answer here.

What is...

What is Hill Order?

Hill Order is a system of writing chemical formulae. If the compound for which the formula is being written contains carbon, the number of carbon atoms is listed first. The number of hydrogen atoms is listed next. Every other element is listed subsequently in alphabetical order.

If the compound for which the formula is being written does not contain carbon, every element (including hydrogen) is listed in alphabetical order.

A list of chemical formulas (e.g. in an index) is compiled alphabetically according to the first element in each formula.

An example of a list:

  1. CNaO3
  2. C6H6
  3. C7H14O
  4. H2O
  5. KIO4
  6. K2S

Resources that use Hill Order

The CAS Registry Number Database CRC Handbook of Chemistry and Physics, Merck Index, and Reaxys all require that Hill Order is used when searching by molecular formula.

What is a Reaxys registry Number?

You can also search compounds by their Reaxys Registry Numbers (also referred to as RX-RNs). But unlike CAS numbers, these numbers do not refer to biomolecules like enzymes or commercial mixtures. These numbers can be used in both Reaxys and Scifinder.

How do I find a registry number?

Search for your for your structure or compound based on the information you have (such as chemical name, molecular formula, etc.) in a resource that contains registry number information.  Some resources to try are: SciFinder, Reaxys, the CRC Handbook of Chemistry and Physics, The Merck Index, ChemSpider, Sittig's Handbook of Toxic and Hazardous Chemicals and Carcinogens, the CAS Index Guide, or the Sigma-Aldrich Corporation website.

What is a CAS registry number?

A registry number (sometimes seen as RN) is a unique identifying number assigned to a chemical compound, commercial mixture, or an entire class of molecules (e.g. categories of enzymes).  A CAS registry number is one assigned by the Chemical Abstracts Service (CAS) once a substance is registered with them. CAS registry numbers are assigned to structures rather than names, and look something like this: 15687-27-1 or 71-43-2.

Why are CAS registry numbers useful?

 Using a registry number allows you to bypass tricky or ambiguous naming conventions when searching for a particular substance. Because CAS is an internationally recognized collection of chemical information, their numbers can be used to find chemical information on a the same specific structure in a variety of databases, indexes and search engines. CAS numbers can be used to generate multiple names of substances, and vice versa.

Note: isomers that have the same molecular formula will each have their own CAS numbers.

How do I use CAS registry numbers?

 

Resource

How to search by CAS Registry Number

Google

Type into search bar

Scifinder

“Explore Substances” > “Substance Identifier” tab

Scopus

“Document Search” > select “CAS Number” from dropdown list

Science of Synthesis

“Query” > “Refine Query”

CRC Handbook

“Structure/Property Search” button

Merck Index

Under “Basic Search” tab

Reaxys

“Substance & Properties” tab > “Substance Data” > “Identification Data”

What are DOIs?

DOI stands for digital object identifier. A DOI looks something like this: 10.1021/ja100167z. They are typically found as part of the citation information for journal articles published in the sciences.  DOIs may also be used for electronic books or book chapters.  A DOI uniquely identifies a publication – no two publications will have the same DOI, and one publication in multiple databases will always have the same DOI.  When you search using a DOI, that particular article will always be the result. This is helpful because it saves you from having to remember the journal title, article title, volume numbers and so forth!

Where can I find a DOI?

A DOI can be found anywhere in a journal article – under the author information or the article title, or at the top or bottom of the first page.  DOIs can also be found in database search results, or by clicking on the detailed record for the article you are interested in.

Do all articles have DOIs?

Some articles may not have a DOI.  For example, articles published outside of the sciences tend not to have DOIs.  An article may also not have a DOI if it was published before DOIs existed (though some older articles will have had DOIs added!).  DOIs are becoming more common in the scientific community, so recently published articles tend to have a DOI assigned to them.  

Using DOIs in databases

DOIs can be used to locate an article in particular databases like SciFinder, Reaxys, Web of Science and SCOPUS.

DOIs can also be searched through Google.

DOI Resolver

Resolve a DOI Name

How can DOIs be used?

Find the full text of an article using the DOI

The purpose of a DOI is to give a distinct alpha-numeric name to an article to allow that article to be uniquely identified without using potentially ambiguous search methods such as journal titles or abbreviations, names of authors, or article titles.

Because of this, you can use a DOI to check if we have electronic access to the full text for a specific article by using the Article Finder.  Article Finder can be accessed through the UTL homepage – it is located below the catalogue search bar on the right.   On the Article Finder screen, there is an option to search specifically by a DOI. Plug the DOI into the box and click search – you do not need to provide any information other than the DOI! This brings up a page that allows you to select the provider you wish to access the full text through. 

Create a permanent link using a DOI

DOIs can also be used to create a permanent link to the article. This is helpful if you want to share the article with someone, or can be used as an easy way to bring up an article in the future. Building a permanent link using a DOI can be done through either of the following methods:

Using Article Finder:

  1. Open Article Finder
  2. Enter the DOI (for example, 10.1021/ja100167z) in the DOI field 
  3. On the next page, a banner will appear at the top that says "provided by the University of Toronto Libraries"
  4. Click the “Get a short URL for this item” link on the top left hand side
  5. Now you have your permanent link: http://simplelink.library.utoronto.ca/url.cfm/125257

This link will take you the page that displays the providers for your article.

Building your own link:

  1. you will need the UTL proxy for you link – this will automatically give you access to University of Toronto electronic journals:
    http://myaccess.library.utoronto.ca/login?url=
  2. add the DOI resolver (http://dx.doi.org/)to this:
    http://myaccess.library.utoronto.ca/login?url=http://dx.doi.org/
  3. add your specific DOI (for example: 10.1021/ja100167z) to the end of the string to create your permanent link:
    http://myaccess.library.utoronto.ca/login?url=http://dx.doi.org/10.1021/ja100167z
  4. Now you have your permanent link:  http://myaccess.library.utoronto.ca/login?url=http://dx.doi.org/10.1021/ja100167z  

This link will take you directly to your article - you will not have a choice of providers (if you are off campus it will ask for your UTORid and password first).

What is an InChl Key?

An InChI is a string of characters used to uniquely identify chemical substances.  This system was developed by IUPAC to make searching for molecular information online easier.  The InChI has been further condensed into a shorter string called an InChIKey.  The InChIKey remains a unique identifier, and can be searched in some database.  An InChiKey can also be plugged into internet search engines such as Google to retrieve information about a particular substance from internet sources.  An InChIKey will look something like this: WPYMKLBDIGXBTP-UHFFFAOYAD

Notice the difference between an InChI and an InChIKey:

 
Image from ChemSpider

Further Information:

 

Where can I use InChlKeys?

  • Google and other search engines
  • ChemSpider
  • SciFinder
  • Reaxys

RSS Feeds

RSS stands for Really Simple Syndication. RSS allows you to pull information from different websites and put it on one page. RSS feeds are “feeds” because as websites are updated the new information is “fed” onto your page providing the most current information from a source you are interested in. RSS feeds give the user quick access to up-to-date information about recent publications and news.

In order to create a RSS feed you need to set-up a “reader”. Readers can be found in email accounts such as gmail and yahoo, on your computer, or on your browser, for example Firefox or Internet Explorer. Readers are also known as aggregators as they aggregate information from multiple sources.

To get started you have to download an RSS Reader or familiarize yourself with the one on your computer. The next step is to find a website on your topic/interest with an RSS feed, usually indicated by an orange “add feed” button.

Many sites will also allow you to add a RSS feed by clicking on the button and then indicating the reader you have.

 

Some examples:

Angewandte Chemie International Edition’s RSS feed
http://onlinelibrary.wiley.com/rss/journal/10.1002/(ISSN)1521-3773

Journal of the American Chemical Society: Latest Articles (ACS Publications) RSS feed
http://feeds.feedburner.com/acs/jacsat

Example of database RSS feed:
Reaxys RSS feed

Alerts

Email alerts are different than RSS feeds.  With alerts, you will receive notification of new information directly to your email account.  With RSS feeds, you will have to check your reader or aggregator.  Alerts also offer you the ability to customize the information you wish to receive instead of just seeing the most recently published information.  By subscribing to email alerts you can receive an email when information on a topic or subject that interests you becomes available.

Many databases and publishers now offer a variety of email alerts to choose from.  For example, content alerts notify you when a new issue of a journal(s) is published from either a selected journal or a database.  Search alerts email you when newly published information related to one of your saved searches is added.  This can include when an article you are interested in is cited or when an author you are following publishes a new article.

Whereas RSS feeds are constantly being updated as new information becomes available, email alerts are only sent when specific information is produced.  The frequency of which you will receive alerts will depend on the type of information that is being requested (i.e. journals issued on a monthly or a bimonthly basis), or on the frequency preference you set for your alerts (i.e. weekly, daily, whenever something new is published).

Setting Up Alerts
(Resource Help Sections)

Scopus: 
“customizing” explains how to set-up different RSS feeds and alerts
Create email alerts for an affiliation

Web of Science:
About alerts and RSS feeds
Citation alerts
Saved search alerts

SciFinder:
Set up a "Keep me posted" alert 

Reaxys:
"Alerting" 

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How do I find information on...

UofT Patent Guide

Other Helpful Guides

 

Patent Searching and Retrieval

pKa Values and Prediction

Finding pKa values

  1. If it is a known compound in Scifinder, use the ACD software to predict properties.
     
  2. There are a few free pKa predictors such as Chemaxon's Marvin (download Marvin) with a free pKa plugin for academics (download pKa plugin)

Another option that is a very good predictor is SPARC (download SPARC)

In a comparison trial SPARC was comparable to ACD: http://pubs.acs.org/doi/abs/10.1021/ci900289x

 

Useful Databases and References

 

SciPlanner

SciPlanner is a CAS research tool, found in SciFinder, that acts as an interactive workspace. It allows users to create customized reaction pathways as well as organize and manage SciFinder results in ways that they find most useful. Users can integrate reactions, experimental procedures, substances, and references from multiple documents” (CAS).

CAS has made the following tutorials available on their website:

Logon to SciFinder (and registration instructions)

What is a masthead?

The masthead is usually located in the first few pages of a journal. It is the portion of the journal that lists relevant information such as, the publisher, journal staff, the reviewers, contributors, subscription information, and addresses. 

How do you find the masthead for ACS journals online?

On the ACS website the mastheads for their online journals are kept in a different section from the articles. To find the masthead go to the "About" drop-down menu in the navigation bar (see the example below) found on the main page of each journal. In the drop-down menu there will be a link to the masthead under "Masthead [PDF]". 

Explanation of the Hammett Equation

Source for Hammett Constants

General Solubilities

Solubility data can be found in a number of different formats. Some reference sources list solubilities of a chemical as Slightly, Very, and Insoluble for various solvents. Other sources will list solubility in g/kg, g/L, weight%, etc at different temperatures.

Some reference books will have both types of data in different parts of the book: for example, the CRC Handbook has basic solubility data in the properties sections at the front of the book but also has more detailed tables further on.

 

Solubility Data Sources

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Subjects: Chemistry