NMR NPE

HI,

the H-NMR predictor fails with MKXZASYAUGDDCJ-JQHSSLGASA-N:

InChI=1S/C18H25NO/c1-19-10-9-18-8-4-3-5-15(18)17(19)11-13-6-7-14(20-2)12-16(13)18/h6-7,12,15,17H,3-5,8-11H2,1-2H3/t15-,17+,18-/m0/s1

 

Clean failed.
[H]c1c([H])c2c(c([H])c1OC([H])([H])[H])[C@@]13C([H])([H])C([H])([H])N(C([H])([H])[H])[C@]([H])(C2([H])[H])[C@]1([H])C([H])([H])C([H])([H])C([H])([H])C3([H])[H]
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at chemaxon.calculations.ui.nmr.NMRPredictionSettings.applySettings(NMRPredictionSettings.java:629)
        at chemaxon.calculations.ui.nmr.result.NMRResultView.setSpectrum(NMRResultView.java:357)
        at chemaxon.calculations.ui.nmr.NMRPrediction$4.run(NMRPrediction.java:252)
        at java.awt.event.InvocationEvent.dispatch(Unknown Source)
        at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
        at java.awt.EventQueue.access$200(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.awt.EventQueue$3.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
        at java.awt.EventQueue.dispatchEvent(Unknown Source)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
        at java.awt.EventDispatchThread.run(Unknown Source)

I recommend to run the whole Pubchem against HNMR and CNMR with

cxcalc hnmr all-pubchem.sdf >all-pubchem-nmr.jdx

I was running only a couple of thousands strucs and I got a couple of failures, mostly/many also with cleaning errors.

 

Cheers

Tobias

Hi Tobias,

Thank you for your error report.

The first molecule is a sequence containing atom list and R group, and it seems that there are additional problems with expanding it.
As a workaround, you may try to give explicite molecules as an input in order to eliminate these sort of problems.

 

For the second molecule (InChi), the C-NMR and the H-NMR works for me. Could you please which version do you use?

But there is a problem with the 3D Clean of the molecule that I could reproduce.
For this particular molecule with the given stereocenters, it is not possible to generate a 3D structure. You can use the stereoisomer plugin to study the problem as it is shown.
There are combination of the signed stereocenters (please find a screenshot attached), which has no corresponding 3D structures. And that is the reason why Clean 3D fails on these particular combinations of stereocenters.

I note that there are two S,S,S structures generated, which only differ in the conformation of the cyclohexane ring. This is a minor bug. Here only one S,S,S structure should be present. The enantiomer R,R,R shows only the chair conformation.

Best regards,

Miklos

Hi Miklos,

all my NMR errors reported are from Msketch 5.11 and the integrated NMR version,

plus Java 7. So maybe these errors are all closed in the newer version which is 6 or higher?

As usual I follow rule, never change a running system, but maybe its time to update again.

Tobias