An Adventure in ChemOffice™ and ChemINDEX
Courtesy CambridgeSoft and Eldest Daughter


L. Van Warren

Friday, June 6, 2003



Today’s review is of CambridgeSoft™ ChemINDEX™, by way of a short saga that out of necessity involved much of the ChemOffice™ toolkit. This illustrated adventure has some unexpected twists and turns, and a surprise conclusion.

Background: I have been a long time user of Cambridge Software’s ChemFinder™ product. ChemFinder™ is one of the great internet science institutions. Name any chemical you can think of, and everything you want to know about it is at your fingertips, courtesy our Massachusetts friends.  Trying to get back out of the box? Just type in any inorganic, organic, or biochemical and you are almost bound to find it using ChemFinder™. But “almost” is the operational term. Sometimes one must make the leap from common to uncommon knowledge. Sometimes the need for that leap can take one by surprise…


My daughter came home from her high school chemistry class with a seemingly simple problem. Create a simple toothpick and foam ball model of 2-bromo-3-methylpropanal. Sounds like that college course, IUPAC 101, which by ancient foggy recipe goes something like:

  • Make a propane
  • Double bond an oxygen to carbon one. This makes propane go propanal.
  • Stick a bromine on carbon two
  • Add a methyl on carbon three. What could be easier?




Well a lot of things probably, but this was the night of the final, and my daughter, showing her usual modicum of due diligence, had also brought the structure home after confirming with the teacher that it was correct. With unwavering faith in the infallibility of her teacher, all that was left was to stick some foam on some toothpicks. There starts the trouble. The approved structure counted for the last and most important 100 points of the semester. The structure and formula were sketched on a napkin in blue ball pen ink. You know the story, “as the goes the final, so goes the class, the semester, the year, the college and career. The sketch of this high stakes game of fate looked something like this:



As a general rule, I stay out of my daughter’s assignments, she is quite low maintenance and only asks question on rare occasions, which is frustrating. I’m happy to build her any size of clock when she asks for the time. But something about this molecule bothered me. I stayed quiet as the foam was painted in non-CPK colors. I even endured temporarily as the model was assembled completely on the flat plane of the table… with carbons lined up like soldiers. But how much can a person take? The errors were piling up. It was time for action, time to do or die, time to speak up for tetradral bonding, to come out of the plane, to break the surly bonds, or at least point them in the right direction! But the greatest teachers, “teach without words”. What to do?


I pointed at the napkin and looked carefully at the name, then at the structure. I started quietly deducting hydrogen’s and thinking bad thoughts like, “Isn’t this a bad drawing of 2-bromo-3-methylbutanal?”



If I would have listened more carefully, I would have heard the distinctive and quiet click that a land mine makes when you step on it. It turns out that to even think of questioning the chemistry teacher is like trying to fool mother nature. It can be done, but its usually not a good idea. My daughter tersely informed me, “…propanal”. But I couldn’t get that fourth carbon out of my mind. I kept counting them over and over, perhaps it was the suffix, perhaps just me. Either way, whether you take the fork in the road or not, that is a butane backbone girlfriend. My elderly blathering interrupted the otherwise pristine concentration of my daughter who was waiting for the white glue to dry. But in the pause I could appeal to a higher authority!  I flipped on my computer, broke out the ChemDraw™ and drew the structure with the primordial wiggles that got carbon going in the first place:



Perhaps this was a “teachable moment”. Perhaps a little tiny tweak of a drawing would open a door of insight never before imagined! Not only could I prove the name was wrong, I could show that carbon structures don’t spend a lot of time in the plane. I quietly went to the name-that-structure feature in ChemDraw™. Convert structure to name I think it was. Instantly I had a labeled structure:




More importantly I had the proof from a higher (and also automatic) authority that my IUPAC piety was indeed deserved, at least in this rare instance. I called my daughter over and showed her the computer applying the name. “Too bad your computer is wrong too”, the denial came. Stunned I reflected, “It must be that my 2D diagram, even with its tetrahedron reminiscent wiggles, is insufficient. I am just perpetuating the myth of the plane myself! Now we have to get the big guns out. Time for some 3D rendering, time for energy minimization and partial charge, time for some real molecular modeling.” I tell my daughter, “Yeah, this is flat picture, on a flat screen, let’s take it up a level”. I save the structure and whip out Chem3D™ Ultra. Time to build a real clock now. That’s easy enough, just read the cdx file:



Now I’m rubbing my hands together. For a warm-up, we need to let this molecule relax into its natural confirmation, complete with steric hindrances. No problem. A little “Minimize Energy” option off the MM2 menu does the trick with lightning speed. The only change? A little double bonded oxygen, leaning back, waiting to catch some rays. I wonder what photon would ring that bond…



The light is starting to shine, my daughter paces uneasily. This could be a problem for her and the teacher and America. Any program like this might just know what it’s talking about. Wait, have you seen the molecules dance? Well they do. Just run a random kinetic motion simulation. Interesting. Most of the rapid motion takes place about a seemingly sluggish Bromine. Mass does count for something. Could it be because Bromine is over six times heavier than los carbones? There’s more. How about charge distribution? At this scale, life is not about geometry, its about charge. What might that look like? Let’s map the partial charges using extended Huckel calculations onto an isosurface.




Now we’re cooking with heat. Then suddenly it happens. The lament begins. My daughter looks at her foam and toothpicks and exclaims, “My teacher is wrong… I can’t believe my teacher is wrong, she has never been wrong about anything ever”.  “Hmm, all this effort to prune by one carbon”, I think to myself. So the teacher missed one carbon among fifty students… that I could do so well. It’s just the process. “So let’s prune by one carbon, verify the name and you can be done. You can turn in your flat model, which is what the teacher wants, and you can also get the chemistry right. All’s fair in learning and exploration.”



With automation in hand we go back and prune by a carbon. We run the names for all the cases. Suddenly an isomeric name pops up, like so, completely unexpectedly, polluting the clear waters of unambiguous names:



Just for grins, we look at it in 3D, to see if the different name is really a different chemical or just a “name isomer”. After all some simple molecules can possess chiral, or handedness. They could be left or right handed versions of each other, like thalidomide that destroys lives, and saves them by cutting off the blood supply in certain cancers.. One racemate prevents infant limb development, the other doesn’t, but that is all an aside. Watching our isomers wiggle courtesy of Chem3D molecular dynamics shows that adjacent groups are free to spin on those single bonds without lockdown from steric hindrance, so our two name­­-isomers are indeed the same substance. We are almost done.



To wrap up would like to know what the differences are between the organic compounds that appeared in our exploration. Is one safe and the other toxic? Do they have common uses? Do they smell bad… or good? One last visit to ChemFinder™ and we should be done. We are now comparing the first and last molecule, the one the teacher drew and the one the teacher named.



We jump to our old friend and type in the names. Neither one of these show up. Could these be rare and exotic compounds? Are they in any web based literature? This is no time to have to trudge down to the library and wade through the chemical abstracts, it is past midnight. This is a job for ChemINDEX™! We can search sketching the structures directly in the web page, or by typing their names. We do both. This search yields 12 compounds that have our first molecule as a substructure and 50 compounds that have our second compound as a substructure. Unfortunately, no references exist by name or by structure for the exact compounds we have encountered. Yikes. The quest is never ending. We will  pursue our exploration even further! Going to Google™, Altavista™ and Excite™ and entering each compound also yields no matches. Who said science wasn’t still young! Ω


Van and eldest daughter reside at a secret lab in the Midwest.


van at