SteinBlog

Computer-Assisted Structure Elucidation by 1D Carbon NMR

We (my group) combined a couple of methods from various of our projects (Bioclipse, CDK, NMRShiftDB, SENECA and LUCY) to create a very simple setup of Computer-Assisted Structure Elucidation. We demonstrated it with the carbon spectrum of a-pinene InChI=1/C10H16/c1-7-4-5-8-6-9(7)10(8,2)3/h4,8-9H,5-6H2,1-3H3

The result is a Bioclipse plugin (bc_seneca) which takes a peak-picking of a measured (experimental) carbon NMR spectrum and a molecular formula as an input. It then uses the CDK deterministic structure generator, generates all possible isomers and predicts carbon shifts for all of them. The result is a list of isomers ranked by similarity of their predicted spectra with the measured one.

[[image:case.png::center:0]]

The correct solution for our test case is a-pinene shown in the upper left corner. Here is also the input CMLSpect file, which is part of the Bioclipse bc_data plugin.

<?xml version="1.0" encoding="UTF-8"?>

<spectrum id="nmrshiftdb10046582" moleculeRef="nmrshiftdb2504"

type="NMR" xmlns:cmlDict="http://www.xml-cml.org/dict/cmlDict"

xmlns:subst="http://www.xml-cml.org/dict/substDict"

xmlns:siUnits="http://www.xml-cml.org/units/siUnits"

xmlns:nmr="http://www.nmrshiftdb.org/dict"

xmlns:units="http://www.xml-cml.org/units/units"

xmlns:cml="http://www.xml-cml.org/dict/cml"

xmlns:macie="http://www.xml-cml.org/dict/macie"

xmlns="http://www.xml-cml.org/schema">

  <conditionList>

    <scalar dataType="xsd:string" dictRef="cml:field" units="siUnits:hertz">Unreported</scalar>

    <scalar dataType="xsd:string" dictRef="cml:temp" units="siUnits:k">Unreported</scalar>

  </conditionList>

  <metadataList>

    <metadata name="nmr:assignmentMethod" content="Unreported"/>

    <metadata name="nmr:OBSERVENUCLEUS" content="13C"/>

  </metadataList>

  <peakList>

    <peak xValue="20.799999237060547" xUnits="units:ppm" peakShape="sharp" id="p0" atomRefs="a9"/>

    <peak xValue="22.799999237060547" xUnits="units:ppm" peakShape="sharp" id="p1" atomRefs="a8"/>

    <peak xValue="26.399999618530273" xUnits="units:ppm" peakShape="sharp" id="p2" atomRefs="a10"/>

    <peak xValue="31.5" xUnits="units:ppm" peakShape="sharp" id="p3" atomRefs="a7"/>

    <peak xValue="31.600000381469727" xUnits="units:ppm" peakShape="sharp" id="p4" atomRefs="a6"/>

    <peak xValue="38.099998474121094" xUnits="units:ppm" peakShape="sharp" id="p5" atomRefs="a4"/>

    <peak xValue="41.0" xUnits="units:ppm" peakShape="sharp" id="p6" atomRefs="a5"/>

    <peak xValue="47.29999923706055" xUnits="units:ppm" peakShape="sharp" id="p7" atomRefs="a3"/>

    <peak xValue="116.0999984741211" xUnits="units:ppm" peakShape="sharp" id="p8" atomRefs="a1"/>

    <peak xValue="144.1999969482422" xUnits="units:ppm" peakShape="sharp" id="p9" atomRefs="a2"/>

  </peakList>

</spectrum>

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Categorised as: Chemoinformatics, Structure Elucidation