Category: Chemistry

TL:DR – A post from 2010 discussing how to draw chemical structures for free. Most likely needs to be updated.

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Chemical structure drawing is of ongoing interest to chemists so we have a list of programs and reviews by users. Of course, with the likes of PubChem and ChemSpider now available one might wonder whether there is any need to draw one’s own structures from scratch, but plenty of chemists and others still do. Sciencebase polled a few contacts via Twitter and LinkedIn to find out what chemical structure packages people are using, what are the pros and cons.

The vast majority of users seem to side with ChemDraw, especially those in academia because of the liberal licensing, but they all gripes about compatibility and cutting & pasting. The likes of ChemSketch fair well and others such as Pymol and Symyx seem to be used by specialists in particular areas.

Wozza told me that he uses ChemDraw, but hates how it’s broken on the Mac and lacks support for that platform, it’s also unfortunate that it has broken round trip editing, and poor cut&paste into other applications. Nevertheless, ChemDraw has good functionality, compatibility with colleagues, and produces “good looking drawings”.

davidperrey uses ChemDraw, as part of ChemBioOffice 2010, though says that he probably draws more structures using Java apps on ChemSpider/Reaxys/etc. “I use ChemDraw for preparing Powerpoint slides or report figures, but most of the time when I am drawing structures (using a computer at least) it is doing literature searches and/or looking up information on chemicals that I am interested in using,” Perrey explains. “ChemDraw is perfectly fine, though I have a pet peeve that when I type an atom in lower case ( say n or cl) it fails to recognize that as the element I am putting in.” As far as the java apps go: Reaxys is the browser-based replacement for Beilstein, so I use it a lot. I find it slow to get started, but once it is going, it is quite responsive and easy to use (except copy/pasting structures takes a while, sometimes easier to just redraw the product). Atom-mapping is useful, but the auto-mapping is occasionally awful — better to do manually.

[Chemaxon’s Alex Allerdyce commented: I think davidperrey was referring to Marvin when he mentioned Reaxys ‘…As far as the java apps go: Reaxys is the browser-based replacement for Beilstein, so I use it a lot…’. So far as I know Marvin is the native editor on Reaxys tho other sketchers (resident at the user — not delivered at the site) are supported.]

Perrey explains that with ChemSpider, “It seems like there are more steps to get down to drawing than there should be, but once you get there, the interface is functional but smooth. All the various rings are hidden away in “templates” but there is a lot to choose from, and simply drawing structures is easy. Atom changes are straightforward too, as you click on the element you want and then just click everywhere you want it.” Then there is eMolecules, which is “mostly for looking for available chemicals, it has a very bare-bones interface, with one panel of tools, but it does the job and has very little load-up time as the Java starts. Labelling atoms is easy, with a fixed list of the most common and a space to fill in your oddballs (it recognizes the elements too, though won’t let you type say zn for zinc, has to be Zn)

He adds that Chem ACX is another for looking for available chemicals, basically a ChemDraw type browser plugin, so similarities to that. Doesn’t like lower case atom labels either. Feels a bit slower and clunkier than the others above.

littleghoti says he uses ChemDraw (despite the price), when he has to because it does all he needs. “But, as a physical chemist, I am deeply suspicious of anything with more than 10 atoms.”

biochembelle also uses ChemDraw. “It’s pretty easy to figure out the basics, even for beginners,” she says, “but has many options available, like a TLC plate drawing tool, templates/clip art for conformers, glassware, complicated ring structures, and it’s easy to generate and modify figures quality and properties, save as multiple file types for publication. It also has the ability to convert chemical names to structures and vice versa. However, the disadvantages are the price but for those who can get an institutional site license. Also, structure and reaction cleanup options are not useful for aesthetics or minimizing space used.

But, chemical informatics expert Wendy Warr, tells me she uses Symyx Draw and its Structure Resolver too. “Symyx Draw is free for personal or academic use,” she adds. Steven Bachrach of Trinity University is also a Symyx Draw user because of the “nice looking drawings, good structure-to-name facility, can produce InChIs, easy to use, free to academics, front end into many database systems.”

Undergraduate detox29 has found ChemSketch to be adequate and gxusm told me that they use Symyx Draw user, mainly because that’s what we were taught to use at University. kjhaxton is also a Symyx Draw user, who occasionally uses ChemDraw or ChemSketch, and Accelyrs DC visualizer & Avogadro for the really pretty graphics!

jat45 uses Chem4Word, ChemDraw, Marvin, JChempaint, and a bit of JME. Jerome Baudry of the University of Tennessee/Oak Ridge National Laboratory, uses Isis Draw or MOE and translate to 2D for “really good looking” structures. Hans Johansson also mixes it up: “Marvin and JChem!” he exclaims, adding that, “The ChemAxxon package is just great and works on most platforms, but ChemDraw is just not worth money, unless you draw and analyze structures all the time.”

Robert Slinn uses ChemBioOffice 12.0 which includes ChemBioDraw which is excellent but not free except to academics. There are a number of free packages available including ACD/Labs ChemSketch and ISIS Draw.

xtaldave uses PyMol and CCP4m, while modernscientist and proteopedia also use Pymol with its Deep View for some structure alterations.

Wozza adds that he looked at Chemdoodle a few months ago and describes it as “very promising, especially with web features, but at the time lacked the functionality to use every day.”

hhhernandez uses ChemDraw as does jordancdarwin if it’s available, but MarvinDraw out of principle.

barneygrubbs laments the fact that all of his old files are in a particular format, therefore, “I sadly use ChemDraw (like @NeilWithers, a former Atoms user for solid state stuff),” he told me. Like others, Grubbs, of Stony Brook University, gave me a list of pros and cons for ChemDraw: Relatively easy to use (now that I’ve been using it for 13 years), exports to other formats reasonably well (.tiff, especially), and has decent layout tools (align, distribute, etc.). But on the downside: Native structures usually look bad when pasted directly into PowerPoint, editing embedded figures in Word sometimes crashes ChemDraw, drawing polymers often requires stretching backbone bonds and using wider bond angles, but there doesn’t seem to be an easy way to do this repeatedly beyond eyeballing the structures. ChemDraw also still has a number of annoyances (cyclopentadiene rings cannot be drawn with a flat bottom bond, many keyboard shortcuts are different from other programs, the C60 default structure looks bad, squiggly single bond is the only real option for generic polymer structures).

“I recently updated my ChemDraw and continue to use it,” Tony Addison, Professor of Chemistry at Drexel University says, “I tried using our free site subscription to ChemSketch (under VMWare Fusion), but the structures I got were of unpublishably poor quality. So I got ChemDraw at an ACS Expo for $90. One thing I find useful about it is the variety of file types to which you can save a diagram for later editing (e.g., in Photoshop).”

Which package you use strongly depends on what you need to draw structures for, says Computational Chemist Richard Wood. “If I am doing docking calculations, then I’d probably “draw” the molecules in Sybyl, as we mostly use SurflexDock to do the docking. If I’m doing QM calculations, then I would probably use GaussView. I’ve occasionally drawn things in Avogadro, but that’s rare. I’ve used ChemDraw in the past, but I’ve noticed that sometimes the structures don’t convert correctly if you want to use them in other applications.” Michael Mayo also explains that he uses GaussView4 as well as generating coordinates with PVWave for Gaussian03 input.

For Drexel University open notebook pioneer [the late] Jean-Claude Bradley it’s ChemSketch all the way, although he recently came across a little issue: “SMILES generated from ChemSketch often don’t work on Daylight or ChemSpider but InChIs generated by Chemsketch work fine (except seem to draw the minor tautomer for all the amides I have been drawing,” he explains.

Like so many others, experienced analytical consultant Bruce Girton says he uses ChemSketch when the terms of the freeware license permit. “I think the drawing interface on ChemDraw is a lot more intuitive than that of ChemSketch, but it’s too expensive for the amount of drawing I do,” he says.

Teaching Fellow Matthew Colo of Harvard University compared the two packages he uses: CambridgeSoft ChemOffice/ChemDraw is powerful, fast, easy to use, has templates to incorporate into structures, and automatic nomenclature (and reverse nomenclature). In contrast, ACD/ChemSketch is free, almost as powerful as ChemOffice, and although it takes a bit longer to use, and there is less automation in drawing, it is still relatively easy to use, has templates to incorporate into structures, and automatic nomenclature (and reverse nomenclature).

Frederick Pruijn, a Senior Research Fellow at The University of Auckland, uses ChemDraw and ChemSketch but prefers the latter because it happens to be the front end for other ACD packages that he often uses. “Our chemists use ChemDraw as their workhorse,” he adds. “They also IsisDraw sometimes but I think that is a little clunky compared to the more “modern” packages.”

Brian Halden echoes the sentiment expressed by most respondents in that ChemDraw outshines the other applications but isn’t free. “I picked ChemDraw because that is all I have ever used,” he says. “I did try MarvinSketch for a while but I found it was still a ways off from being my choice of software. ChemDraw was great for drawing reaction schemes and pushing arrows. It even had some graphics for lab equipment that I had used it the lab so all-in-all, it was the preferred program.”

Jayshree Bhatt, Senior Associate at InnovarIP Consulting Group, adds, “I am a scientist and also draft patents where I draw chemical schemes. I have used both ChemDraw and Symyx Draw. ChemDraw is a good tool for scientists, so is ACD draw which gives predicted NMR values, bond lengths etc, but both are paid software. For the ordinary task of simply drawing structures, Symys is fine as this can be freely downloaded and is compatible with most other software.”

Several correspondents mention checking out SourceForge on a regular basis for updates to the likes of JMol and for newly emerging chemical structure drawing packages and molecular viewers.

Programs mentioned in this post:

The LinkedIn Q&A session is now open again, if you wish to contribute to this post or else you can leave a comment here or on Twitter.

Sceptical Chymist tells me (via Twitter) that they were enjoying the favourite things about chemistry meme started by ChemJobber and continued by Azmanam (known to Sciencebase readers for his chemical spelling dictionary and the C+EN team. As is the wont of meme creators, you pay it forward and have to come up with your own “list” or whatever.

Skeptical Chymist had, “The smell of ethyl acetate (in the morning)”, Peter Atkins’ textbooks, the elements song, and freaky glassware and the prowess of glassblowers on their list of ten favourite things about chemistry. They then passed the baton on to the Chemistry World gang, Michelle Francl of Culture of Chemistry, their Boston- and Tokyo-based teammates Steve and Anne, and yours truly.

Now, I usually don’t bother with the generic memes (unless it’s one I’ve come up with myself) but how could a chemist resist a chemical meme? Unfortunately, several of the things I thought about putting on my list, like Tom Lehrer’s The Elements Song have already been listed by by meme predecessors. So, I thought I’d do something slightly different and list my favourite compounds in no particular order:

• C₆₀
• C₂H₅OH
• C₁₂H₁₇NO
• C₁₃H₂₁NO₃
• C₂₇H₄₄O₆
• C₁₂H₂₄O₆
• NO
• H₂O
• NaCl
• H₅IO₆

As with all of these kinds of memes, one has to pass it on, so I’m nominating ChemistPD, Jon Edwards, and Egon Willighagen

The Alchemist travels back billions of years to the dawn of life this week to learn how aspartic acid may be the crystal Eve, the mother of all chirality while heading back to the future also discovers how biology and nanotechnology might be fused to produce new metamaterials for a range of medical and analytical technologies. Banned scent compounds turn up in childrens toys, we hear while US chemists have built a molecule that bites its own tail to trap smaller molecules within. In environmental news, the recent volcanic activity that grounded thousands of travelers to and from Northern Europe may not have the environmental impact some observers have suggested. Finally, chemistry is the word as Microsoft launches a CML, chemical markup language, add-in for its well-known word processing application.

The Alchemist Newsletter

Delicious links March 16-18

• Chemical Science – Building linear polymers from monomers, inaugural paper in RSC's new journal
• Bing maps now let you scan the nighttime sky – The stars are coming out tonight…even when it's cloudy
• Sex and social networking – Patterns of prostitution revealed by analysis of social networking site has important implications for spread of sexually transmitted diseases.
• 7 steps to restore trust in science – Every journey begins with a single step, here's the seventh to restoring public trust in science
• Malevolent Design: The Death of a Loving God – Never before has a book so aggressively levelled the charge that a creator deity, if it were to exist, would be completely and unimaginably evil. Darwin said it first when he talked about parasites, but think opium poppies, oral cancer, spina bifida, famine, malaria, ebola…where's the intelligence in any of that?
• Breaking Bad – Every chemist's favourite TV show returns with a third series in March 2010 BrB -bromobismuth ?-)
• science – Ten Word Wiki – Learning by prediction and observation instead of making sh*t up

UPDATE: Please let us know – which element are you?

Teaching chemistry has changed so much since my day. This classic Youtube clip highlights the way the elements might interact at a periodic table party. Carbon is popular with the hydrogens, the noble gases are the emo wallflowers, but it’s the fight that breaks out between potassium water that even had my teenage son laughing. Check out the chemistry, or lack thereof, between hydrogen and neon…