A comparison of six chemical drawing packages A chemical drawing package is an essential part of any chemist’s software collection and there are now an increasing number of alternatives ranging from free to very expensive. Chemists become very attached to a particular package and in an ideal world would prefer to use the same package for creating publication quality structures for manuscripts, as the front-end to query databases and as a front-end to chemoinformatics tools. Unfortunately it seems that every database uses a different drawing package and learning the quirks and limitations of each package is tedious. Interestingly ChemSpider structure searching (http://www.chemspider.com/StructureSearch.aspx) now offers a range of six different chemical drawing packages to allow the user to choose their favoured package. It also provides the ideal opportunity to compare the different chemical drawing packages side be side. If you go to the ChemSpider structure search page, and then click on the chemical structure a new window opens, there is the option to enter a text identifier such as a SMILES string or CAS Number however if you click on the “Draw Structure” tab you will be taken to the chemical drawing page. ACD Labs/SDA The default seems to be ACD/Labs SDA (Structure Drawing Applet) which is shown below, this is a Java app and for security reasons you will be required to give approval depending on your download speed the application may take a few 10s of seconds to appear. The alternative drawing packages can be accessed using the radio buttons at the bottom of the page. ACD Labs/SDA is a well established application and to be honest the interface now looks rather old-fashioned, and it is sometimes difficult to see which of the buttons is chosen (which can lead to drawing a structure based on bromine atoms!). To draw structures simply click on a particular atom type and then simply click and drag to create atoms and the joining bonds. To change an atom type you choose a different atom from the left hand column and then click on an atom in the structure, unfortunately ACD Labs/SDA does not support keyboard entry to change atom types which I find very useful, you also can’t select multiple atoms and change all to the same atom type (eg when drawing CF3). There is also a periodic table to choose less often used atom types. The Radical Table (highlighted in red) gives access to a wide range of functional groups, you then simply click to add these to the structure. This works fine for most groups but I’d not be happy with the way nitro groups are displayed. In theory templates should be available from the “Templates” button but I found it only opened an empty window. Reading the manual it does seem that creating fused structures involves a rather convoluted process. A couple of things I found slightly irritating 1) when you open the periodic table or radicals window you can’t edit anything in the main window until you close the other windows and 2) I find colour coding heteroatoms very useful. 3) The “Clean Molecule” function expands the structures to fill the window, so if you use it to clean a structure halfway through drawing it becomes difficult to see further additions to the structure. Symyx JDraw This is another Java application but the interface looks cleaner and more modern, although the letters on the atom type buttons at the bottom of the drawing panel and on the templates in the upper bar are rather small.
The choice of chemical drawing package is a very personal choice but I tend to favour the non-Java applications simply because they can be used on mobile devices such as an iPad. At the moment Elemental appears to be a much more fully featured than Ketcher.More Reviews and Tutorials