Chemical Structure Drawing Software

by David Bradley

"I made this drawing in less than five minutes, but it took me sixty years to be able to do that"

-- Pierre-Auguste Renoir (1841-1919)

 

Click here, for a list of current chemistry drawing software packages most of which allow you to calculate molecular weight for the structures that you draw.

Sketchbook Chemistry - Chemists think in pictures, structures are all. It comes as no surprise that chemical-drawing packages are among the most popular software components available. Indeed, ACD/Labs own ChemSketch had, at the time of writing, reached its 341,320th download in less than six years since the launch of the freeware version. So, what makes chemical sketching such a valuable tool for chemists and others whose research touches on this underpinning science? David Bradley reports on the views of ChemSketch users.

"I saw a colleague using ChemSketch, and became amazed by its simplicity," Barbaros Akkurt of the Turkish Chemical Society told us. Carlos Franco PhD of the Department of Chemistry at the National Pedagogical University of Colombia echoes the sentiment, saying that ChemSketch is "an excellent free software package that users can apply either in the classroom or in their chemical research." Clyde Metz of the Department of Chemistry and Biochemistry at the College of Charleston came across ChemSketch at an American Chemical Society meeting via a demo disc in action. "As new versions were released, I kept up to date." Metz has an academic site license for the department so that his students can use the structure building features for copying over to lab reports, papers, etc.

ChemSketchIt is easy to see why ACD/Labs has such a rapidly growing number of followers for its ChemSketch program. With the freeware version 5.0 of ChemSketch, users can draw molecules freehand, build their structures from a wide range of ready to use templates or import various standard chemical structure formats and modify them to their own needs. For instance, it is possible to import and export ChemDraw, ISIS Sketch, MDL molfile, and SMILES strings. ACD/Labs describes the process as "click and draw molecules" with ions, stereo-bonds, text, polygons, arrows, etc., all readily available. Once a molecule is complete, users can automatically calculate molecular weight and formula, display estimates of density, refractive index, molar volume, and many other useful parameters.

"I've encountered no difficulties in getting used to the software," says Akkurt. He adds that the best feature of the package is its 3D optimization, although the IUPAC naming facility comes a close second. "The IUPAC naming service is very nice," he adds, "as many other programs cannot recognize a number of special organic radicals." Akkurt goes on to explain how ChemSketch has helped him greatly in quickly processing elemental analysis data for various organic compounds as well as producing their IUPAC names. "ChemSketch allows me to produce reliable structures quickly," he says, "I don't use nor need to run any other program." Interestingly, while he uses the ChemSketch Draw mode mainly for chemistry-related sketches, he has also found it amenable to creating non-chemistry structures, such as organization trees too.

The freeware version also includes the tautomers module, dozens of templates, the 3D viewer program and one of the most interesting features, the Name Freeware Add-On, which allows users to convert a structure into an IUPAC name for their molecule. For users who opt for the full version, ChemSketch includes the ACD/Dictionary module, which contains more than 125,000 systematic and non-systematic names of structures and so can speed up the structure-drawing process considerably.

There are many specialist users too. "I first saw ChemSketch at a meeting of the American Society for Mass Spectrometry," says David Powell, Director of Spectroscopic Services in the Department of Chemistry, University of Florida at Gainesville, where a number of groups use ChemSketch. "I found ChemSketch a little easier to learn so the learning curve was faster," says Powell, "ACD/Labs also gave us the ability to import a structure directly into our sample submission form for mass spectrometry, working with us to set up a macro in ChemSketch to do this." Powell is also enthusiastic about one of the program's specialist features which can be purchased as an add-on, "I really like the MS Fragmenter routine," he told us, "which allows prediction of fragment masses and structures, this is very useful for interpreting unknown mass spectra."

ChemSketchAnother specialist user is forensic toxicologist Chip Walls, Technical Director of the Department of Pathology at the University of Miami. He first saw a favorable review on the Web about chemical drawing programs that did a nice comparison. "I downloaded the free version of ChemSketch and found it much easier to use," he said. He was so impressed, he bought the full version with the dictionary. "With each revision I grow more attached to the ease of use and the ever expanding dictionary," he added. The many more import and export features and the dictionary are major advantages over other packages and keep Walls coming back for more. "I use the structures in my procedures and in talks I have to present," he explained, "I export the drawings in windows metafile format (WMF) and can insert them as a picture in just about any application. You can change color of the structure easily making it a snap to insert into PowerPoint slides with colored backgrounds." He adds that the WMF is small, fast to load and easy to keep within a presentation. "Of course, you can also insert the ChemSketch file and link to it to keep it up to date with any changes," he adds.

Some users do not take to ChemSketch immediately, Tamas Gunda of the University of Debrecen in Hungary, for instance, gave the program a quick try after finding it on the Internet. It was only later when he did a probing review of chemical drawing applications that he began to see its advantages over other packages. "The freeware version contains more features than other free chemical drawing applications," he says, and although every application has its strong and weak sides, one of the big pros of ChemSketch is in making poster-sized drawings. Gunda adds, "In my experience, ChemSketch is best for joining chemistry and other pictures together for direct printing or transferring to a general drawing package in Windows Meta Format."

Metz adds that the free 3D viewer is also a rather attractive feature, "I realize that this is the front-end for other programs which we don't have, but it is for student use and works fine," he explains. Indeed, ChemSketch has become an integral part of the curriculum for the College's NCSI/CCCE workshops to show and let people work with it. "For what is in the free version of ChemSketch/3D Viewer, it is done well," adds Metz, "and for someone with no funding, it is a way to introduce a little molecular modeling and visualization into an undergraduate course."

Funding levels are an important consideration for many users. Franco admitted that finances are a main driver in choosing software in a country where resources are limited: "The primary advantage over other similar packages is that the free version of ChemSketch is fully functional in all its options." That said, Franco points out that all users can view models in 3D dimensions, with animation or from different perspectives. "The ChemSketch drawing tool is an easy way to make presentations, make templates and export images to a word processor, for instance."

"As a teacher of 16-18 years olds," adds British educator Steve Lewis, "I was looking for a quick means of producing simple structures. The initial attraction of ChemSketch was the freeware version!"

While some users rely on the more advanced features, others, including Lewis, have relatively unsophisticated needs for their chemical-drawing software. ChemSketch, he says, meets these well, "ChemSketch itself is not unsophisticated, rather, it's designed well enough that I can use it to my advantage without being overwhelmed by too much functionality intended for more advanced purposes." Having said that, he adds that he is "very impressed by the 3D viewer facilities," which he uses for school 'open' event displays.

ChemSketch 3DChemSketch is downloaded from the ACD/Labs website at a rate of about 300 copies every day and every single country in the world has downloaded it at least once! At the time of writing, the Top 5 countries by number of downloads were USA (>67,000), Germany (>23,000), Canada (>15,000), United Kingdom (>14,000), and China (>11,000). There have even been almost 200 downloads from users in the Vatican City State domain! There are thousands of others in many different countries from the Philippines to Puerto Rico via Antarctica showing just how chemistry brings nations together.

ChemSketch users also have the ability to interact with the software itself through the freeware Programming Language for the Freeware ChemSketch (http://www.acdlabs.com/products/chem_dsn_lab/chembasic/). More than 15,000 users have downloaded the language, which forms the basis of the popular ACD/Goodies. ACD/Labs updates these user contributions to the program store regularly. (http://www.acdlabs.com/products/chem_dsn_lab/goodies.html).

ACD/Labs remains at the cutting edge of structure drawing and visualization including the first structure drawing applet (freeware version at http://www.acdlabs.com/download/sda.html) and recent PDA-based tools (http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/chempalm/). Site licenses of the commercial version of ACD/ChemSketch v5.0 are currently being donated to any interested academic institution (http://www.acdlabs.com/educators/chsk_licenses.html).

This article was originally commissioned as a promotional feature article by ACD/Labs, creators of ChemSketch and Reactive Reports. - ChemSketch - Elemental Discoveries - 08/04

Read the Chymical Wedding List - bonus feature in Issue 71 of Elemental Discoveries; we've also got a new feature listing the elemental discoveries timeline. An update on my position regarding chemical structure drawing software.

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