Archive for November, 2013

We previously reported an initial proof of concept of an “Insert from ChemSpider” TinyMCE plugin which was integrated with Southampton University’s ELN LabTrove to add compound images from ChemSpider to posts. We are pleased to announce the version 2 of that plugin which now allows a bench chemist who is planning or reporting a reaction to construct a stoichiometry table of the chemicals used and produced in it, as shown at the bottom of this post. Constructing one of these tables manually can be a tedious and error prone task, but now when a LabTrove user is writing up an experiment post about a reaction, they can click on the “Insert from ChemSpider” TinyMCE plugin button in the editor which guides them through the task and retrieves compound properties from ChemSpider so that they don’t need to draw out the compound, or type in its name, molecular weight or formula mass. The amount of each substance can be expressed in a number of different ways – ratio (equivalence), number of moles, mass or volume (depending on the compound state and reaction role), and the user only needs to enter one of these properties and it is automatically inter-converted into the other relevant properties (including calculating equivalents). The product yields are also calculated (as the percentage of the amount actually recorded compared to the amount calculated from the ratio of the product and the amount of the limiting reactant).

Another feature is that it is possible to construct advanced stoichiometry tables which are initially created during a planning stage (during which planned amounts of reactants and products are entered and calculated), but with a separate column to add actual amounts of reactants and products at a later stage.

This functionality was used as part of the intern project to share compound and reaction data in LabTrove and ChemSpider to create an example reaction page in LabTrove. The top of that page was made using the ChemSpider Reactions template, and the table at the bottom with the “Insert from ChemSpider” plugin.

A demonstration video showing how to use this new functionality is shown below:

The TinyMCE plugin relies on the new ChemSpider “Edit Stoichiometry Table” jquery widget which contains all of the functionality behind it. The widget can be used independently of LabTrove, for example in a ChemSpider widget example page, and as such can be easily integrated into different ELNs and websites. We will also be using it in conjunction with the imminent ChemSpider Reactions platform to allow upload of stoichiometry table data to be hosted on there with other reaction data. To allow the widget to be flexible and used by different applications for different purposes, after a stoichiometry table has been created, the widget allows it to be retrieved either as pure html, or a json string (which can be accepted as an input option for the widget to display and edit an existing stoichiometry table) or a html table with the json embedded as a data attribute in it. The latter option allows a stoichiometry table to be added to a webpage with the option to edit it at a later point.

This is the first version of the edit stoichiometry table widget, and it will be used and tested and revised accordingly. Further developments are also planned for the “Insert from ChemSpider” TinyMCE plugin used in LabTrove.

If you would like to to integrate the ChemSpider “Edit Stoichiometry Table” widget with your website, web-based ELN, TinyMCE editor (e.g. WordPress), or LabTrove installation to use and test it and provide us with feedback then please contact us at chemspiderdev@rsc.org.

Output of ChemSpider “Edit Stoichiometry Table” widget: Stoichiometry Table of Substances Used/Produced

Compound Information Substance Information Planned Amounts Actual Amounts
ChemSpider ID: 9162369
Name: 5-Iodo-1-pentene
Formula: C_{5}H_{9}I
MW: 196
compound image
Safety Information:
Role: limiting reactant
State: solution
Source:
Molarity: Moles/L
Concentration: 7.95 g/L
Solvent: THF
Comments:
Ratio: 1.00
Amount: 0.00500 Moles*
Mass: 0.980 g
Volume: 0.123 L
Ratio: 1.00
Amount: 0.00500 Moles*
Mass: 0.980 g
Volume: 0.123 L
ChemSpider ID: 7789
Name: 3,4-Dihydro-2H-pyran
Formula: C_{5}H_{8}O
MW: 84.1
compound image
Safety Information:
Role: reactant
State: solution
Source:
Molarity: 11.79 Moles/L
Concentration: g/L
Solvent: THF
Comments:
Ratio: 2.80
Amount: 0.0140 Moles*
Mass: 1.18 g
Volume: 0.00119 L
Ratio: 2.80
Amount: 0.00750 Moles*
Mass: 0.631 g
Volume: 0.000636 L
ChemSpider ID: 10254347
Name: t-BuLi
Formula: C_{4}H_{9}Li
MW: 64.1
compound image
Safety Information:
Role: reactant
State: solution
Source:
Molarity: 1.7 Moles/L
Concentration: g/L
Solvent:
Comments:
Ratio: 1.60
Amount: 0.00800 Moles*
Mass: 0.512 g
Volume: 0.00471 L
Ratio: 1.60
Amount: 0.00600 Moles*
Mass: 0.384 g
Volume: 0.00353 L
ChemSpider ID: 29341335
Name: 6-(4-Penten-1-yl)-3,4-dihydro-2H-pyran
Formula: C_{10}H_{16}O
MW: 152
compound image
Safety Information:
Role: product
State: liquid
Source:
Purity: 100%
Comments:
Ratio: 1.00 *
Amount: 0.00500 Moles
Mass: 0.761 g
Ratio: 1.00
Amount: 0.00456 Moles*
Mass: 0.694 g
Yield: 91.2 %

(* indicates entered value)

We have just uploaded three new short video tutorials walking you through how to search, comment on, and submit ChemSpider Synthetic Pages procedures.

An introduction to searching ChemSpider Synthetic Pages

Reading and commenting on ChemSpider Synthetic Pages articles

Learn how you can share your work on ChemSpider Synthetic Pages

We welcome any feedback, as well as suggestions for topics for new help videos.