From a user
I did several calculations (pKa, cLogD, cLogP, isoelectric) on a number
of antibacterials at the end of April - finishing on May 1 - and
presented a bit of it in a seminar I gave. Today, I was redoing some
of thosae calculations (as I had some questions) - and found that for a
number of compounds, the calculations (obviously based on the pKa calcs
used) had changed - specifically for ciprofloxacin, tetracycline and
sulfaguanidine. The calculations now generally conform to the ACD (at
least the cLogD 7.4 and cLogP) whereas previously they were quite
Did something change in the way the calculations were done
between May 1 and 14th? Are they stable now? I did update my Java
between those 2 dates (and now I get some new error messages and I
can't do cLogPs) - could that have affected the calculations (I really
...at the end of April - finishing on May 1..
Please send the version number of that calculators.
Today, I was redoing some
Please send the version number of the calculators you have today.
I get some new error messages
What is the error message?
Sorry it took me so long to answer.
I don't know the version number of Marvin that I was using, as it was the website Marvin, Calculator Plugin and Chemical Terms Demo (http://www.chemaxon.com/marvin/sketch/index.php) - and I can find no version # there. So whatever version was running the demo between April 26 or so and May 1 was the first version. The calculations were changed when I used it May 14th. As mentioned in the original note, the pKa graphs, microspecies - and hence the cLogDs and charge distribution, for at least 3 compounds changed: ciprofloxacin, tetracycline and sulfaguanidine. A number of others did not. Cipro and tet have multiple protonatable sites and are pretty complex. The cLogD at pH 7.5 for cipro started at -3.3 and, in the later version, went to -1.39 (much closer to the ACD cLogD at 7.4). I did not note the actual pKas for each protonatable site, so I don't know if those were what changed or the calculations used on them. I'm a microbiologist, not a chemist - so don't get to complicated with the explanations for me. What I want to know is in general what changes were made and if they will be stable. I may want to use a set of calculations in a publication so I want to know what Marvin version to refer to.
About the error messages. I'm ataching a word.coc with a screen capture showing 2 messages. The small one has appeared since I started using ChemAxon with both an older and an updated version of Java. It doesn't make any difference - the thing works OK. But the larger message saying that your code isn't certified (or somesuch, I'm not reading it right now) started with the Marvin version extant on May 14th - which coincided with my having updated Java. (so I don't know whether it was do to a change in code or a change in Java).
Version info about the calculators:
April 26: version 5.3.2
Maj 14: version 5.3.3
A few changes occured in respect of the handling of the hydrogen bonding of certain "OH" and "=O" groups in the pKa calculation.
Yes, the new version seems to be stable.
I have attached a file from the structures you talk about. Both tetracycline and sulfaguanidine have different tautomer structures and their logD profile will be different. Please take into account this ...
I don't have experimental results.
But the larger message saying...
This message confirm you that everything seems to be OK with the application you are about to run. You can find further explanation on the wikipedia from this topic.