LogP of isomers

User 247a2c5018

02-04-2009 08:56:15

I have two isomers and the calculation of Logp give me 2 different results?

Why? In the last version of MarvinBeans (4), the 2 LogP are the same.

User 851ac690a0

03-04-2009 13:46:21


"Isomer1" and "isomer2" are  tautomers of each others.  Since their structures are different this is why their calculated logP (based on molecular topology) will be different as well.

Identical logP value will be calculated if you switch on the "Take major tautomeric form"  option.

(Please note that your attached files "isomer1" and "isomer2" are identicals.)


User 247a2c5018

03-04-2009 14:08:07

sorry i correct isomer2.mol

User 851ac690a0

03-04-2009 14:58:56


Ok, thanks.


User 247a2c5018

06-04-2009 08:58:00

Normally, I calculate Logp with :


cxcal -N hi test.sdf logp -p 3


I try to add the option M  but it doesn't work.

If I try only :

cxcalc logp -M isomer1.mol

it works but I would like to remove the id


cxcalc logp -M N hi isomer1.mol => doesn't work

User 247a2c5018

06-04-2009 09:00:55

Ok I find :cxcalc -N hi logp logP -M isomer1.mol -p 3



User 247a2c5018

06-04-2009 09:01:56

correction : cxcalc -N hi logp -M isomer1.mol -p 3

User 247a2c5018

15-04-2009 09:15:02

cxcalc -N hi logp -M isomer1.mol -p 3 is correct?

or cxcalc -N hi logp -M true isomer1.mol -p 3 is correct?

ChemAxon e08c317633

15-04-2009 09:27:07

Both are correct. In case of [true|false] parameters true can be omitted.


User 247a2c5018

15-04-2009 13:10:14

I have problem with the structure joined.

cxcalc -N hi logp -M 2008-10-30_6_L.mol -p 3 => the time of calculation is too long


If i remove the "-M", the time of calculation is normal

User 247a2c5018

16-04-2009 12:44:48

No idea?

So I remove the option M of my calculation of logP

ChemAxon e08c317633

17-04-2009 10:19:08

It is a quite large molecule, and calculating the major tautomer of a large molecule takes time. Without the tautomer calculation (-M option) it is much more faster.

Anyway, it seems the tautomer calculation in this case is really slow, so we will check it.