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ChemDraw Making Life Easier for the Medicinal Chemist
Jeroen Verheijen, Ph.D.
Dr. Jeroen Verheijen studied chemistry at Leiden University in the Netherlands where he received
his M.S. and Ph.D. degrees in chemistry. In 2000, he moved to Providence, Rhode Island to accept
a position as head of the medicinal chemistry department at Sention Inc. Founded in 1999, Sention
is a pharmaceutical development company focused on the discovery and development of drugs to
treat memory impairment and other central nervous system disorders.
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When i was writing my Masters' thesis in 1994, I used a software application named PLT51 to draw
the chemical structures. The version that I had was so old that it was not compatible with the
use of a mouse. I remember the tedious process of navigating the cursor across the screen using
the arrow keys. I had to alternate between cursor moving speeds to obtain the desired accuracy,
and avoid having to wait several minutes, for the drawing of a single line.
The Ultimate Drawing Application
I thought that I had died and gone to heaven when I started my Ph.D. research in 1995 and my group
provided me with a copy of ChemDraw Pro 3.5. I could do anythingÑthe program worked with my mouse,
it came with templates and automatically adjusted the settings of my drawings to conform to the
guidelines for the journal of my choice. This had to be the ultimate chemical structure drawing
application. I still thought so until I had the opportunity to evaluate ChemDraw Ultra 7.0.
ChemDraw Ultra comes with ChemFinder Pro and Chem3D Pro. Although these are also great products,
I will focus this review on the ChemDraw application. The software development team at
CambridgeSoft found some room for improvement in an already great product. Some of these
new aspects of the software have come in handy in my new work environment. I now work as
director of the medicinal chemistry department in a small biotech/pharmaceutical start-up.
As such, I have to work closely with a variety of people. I work with our molecular biologists
on the evaluation of early preclinical lead compounds, with our behavioral scientists on the
evaluation of advanced lead compounds, and with our clinical team and outside contractors on
the clinical supplies.
Fully Integrated
Different people use different software applications and non-chemists usually have no need to
purchase a chemical structure drawing application. However, this is not a problem as ChemDraw
is now fully integrated with other Windows applications. I can edit structures within any Windows
application simply by double-clicking the structure. No more need to find the original file, make
a modification, save the structure file, and copy and paste it into a document to share with my
colleagues.
ChemDraw's integration with Microsoft Excel is a definite advantage. In Excel, you can insert
a ChemDraw worksheet that contains structures and other data (such as data from biological assays).
Structures are contained within a cell and you can toggle between displaying the structure or the
name of the compound. ChemDraw also allows you to search for a structure within an Excel document.
More importantly, your non-chemist colleagues, who may not own a copy of ChemDraw, will be able to
work with your Excel document and see the structures that you have created.
Right-Click Menu
Another Windows integration feature is the right-click menu. As in many other Windows applications,
right-clicking in a ChemDraw document will now bring up a short list of commonly used ChemDraw
commands. The right-click menu comes in handy while using one of the other new toolsÑtable drawing.
ChemDraw now lets you draw a table, drag in structures and text and, by right-clicking, you have
single-click access to features such as automatically resizing the table to fit the contents or
editing the appearance of the borders.
Tables
In the past, I have tried to create tables in other Windows documents by dragging chemical
structures into the table using copy and paste. However, since tables in word processing applications
are designed to work with text, I would run into many problems trying to create tables containing
structures. With the new table tool in ChemDraw, I now have the ability to create a table in
ChemDraw, manipulate it, and then copy it into another application. Even better, is the fact
that double-clicking in that application allows you to edit the contents of the table again.
Improved User Interface
In addition to these improvements, ChemDraw Ultra 7.0 also contains new functions that are very
useful in creating structures. ChemDraw recognizes stereochemistry and will infallibly provide
you with the correct stereochemical assignment of a structure. While drawing an alkyl-chain,
ChemDraw will show you how many carbon atoms have been drawn. Also very useful is the AutoNom
function where ChemDraw will provide you with the IUPAC name for any drawn structure. This
great feature works in both directions. ChemDraw can also draw a structure for any name that
you supply.
Finally, there are several other new features that make life easier for the medicinal chemist.
ChemDraw documents can now contain multiple pages, thus eliminating the need to save multiple
documents. The structure analysis function has been expanded to include m/e ratios for different
isotopes, in addition to molecular weight and exact mass. This new capability makes it easier
to relate mass spectra to structures. Chemical properties such as melting point, boiling point
and logP are also easily calculated. ChemDraw can calculate chemical shifts for proton and
carbon NMR and display the corresponding spectra.
Templates
This current version contains a variety of standard drawing templates, such as special characters.
You no longer need to go into the ÒfontÓ menu and change to ÒsymbolÓ. BioArt contains items such
as cell membranes, proteins and more, while ClipArt is an extensive set of glassware
and equipment.
For those of us with Internet access, the Online menu provides helpful links to information and
suppliers for selected chemicals. Although the database is rather limited, access to the full
database comes with two other Chem-Office products: ChemInfo and ChemACX Database.
These are just some of the new features in ChemDraw Ultra 7.0. The fact of the matter is that
the software engineers at CambridgeSoft have managed to significantly improve a product that
I thought could not be improved. Working with this latest version of ChemDraw has made me
question how I ever survived without these improve-ments. It just makes you wonder what they
will find to do for version 8.0. For this reason, I rate the software a 5 out of 5.
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