{"id":16,"date":"2007-01-31T12:42:00","date_gmt":"2007-01-31T10:42:00","guid":{"rendered":"http:\/\/www.steinbeck-molecular.de\/steinblog\/?p=16"},"modified":"2007-09-06T10:09:25","modified_gmt":"2007-09-06T08:09:25","slug":"computer-assisted-structure-elucidation-by-1d-carbon-nmr","status":"publish","type":"post","link":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/2007\/01\/31\/computer-assisted-structure-elucidation-by-1d-carbon-nmr\/","title":{"rendered":"Computer-Assisted Structure Elucidation by 1D Carbon NMR"},"content":{"rendered":"

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<\/span><\/a><\/p>\n

<\/p>\n

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.<\/p>\n

[[image:case.png::center:0]]<\/p>\n

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.<\/p>\n

<?xml version=\"1.0\" encoding=\"UTF-8\"?><\/pre>\n
<spectrum id=\"nmrshiftdb10046582\" moleculeRef=\"nmrshiftdb2504\"<\/pre>\n
type=\"NMR\" xmlns:cmlDict=\"http:\/\/www.xml-cml.org\/dict\/cmlDict\"<\/pre>\n
xmlns:subst=\"http:\/\/www.xml-cml.org\/dict\/substDict\"<\/pre>\n
xmlns:siUnits=\"http:\/\/www.xml-cml.org\/units\/siUnits\"<\/pre>\n
xmlns:nmr=\"http:\/\/www.nmrshiftdb.org\/dict\"<\/pre>\n
xmlns:units=\"http:\/\/www.xml-cml.org\/units\/units\"<\/pre>\n
xmlns:cml=\"http:\/\/www.xml-cml.org\/dict\/cml\"<\/pre>\n
xmlns:macie=\"http:\/\/www.xml-cml.org\/dict\/macie\"<\/pre>\n
xmlns=\"http:\/\/www.xml-cml.org\/schema\"><\/pre>\n
  <conditionList><\/pre>\n
    <scalar dataType=\"xsd:string\" dictRef=\"cml:field\" units=\"siUnits:hertz\">Unreported<\/scalar><\/pre>\n
    <scalar dataType=\"xsd:string\" dictRef=\"cml:temp\" units=\"siUnits:k\">Unreported<\/scalar><\/pre>\n
  <\/conditionList><\/pre>\n
  <metadataList><\/pre>\n
    <metadata name=\"nmr:assignmentMethod\" content=\"Unreported\"\/><\/pre>\n
    <metadata name=\"nmr:OBSERVENUCLEUS\" content=\"13C\"\/><\/pre>\n
  <\/metadataList><\/pre>\n
  <peakList><\/pre>\n
    <peak xValue=\"20.799999237060547\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p0\" atomRefs=\"a9\"\/><\/pre>\n
    <peak xValue=\"22.799999237060547\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p1\" atomRefs=\"a8\"\/><\/pre>\n
    <peak xValue=\"26.399999618530273\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p2\" atomRefs=\"a10\"\/><\/pre>\n
    <peak xValue=\"31.5\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p3\" atomRefs=\"a7\"\/><\/pre>\n
    <peak xValue=\"31.600000381469727\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p4\" atomRefs=\"a6\"\/><\/pre>\n
    <peak xValue=\"38.099998474121094\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p5\" atomRefs=\"a4\"\/><\/pre>\n
    <peak xValue=\"41.0\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p6\" atomRefs=\"a5\"\/><\/pre>\n
    <peak xValue=\"47.29999923706055\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p7\" atomRefs=\"a3\"\/><\/pre>\n
    <peak xValue=\"116.0999984741211\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p8\" atomRefs=\"a1\"\/><\/pre>\n
    <peak xValue=\"144.1999969482422\" xUnits=\"units:ppm\" peakShape=\"sharp\" id=\"p9\" atomRefs=\"a2\"\/><\/pre>\n
  <\/peakList><\/pre>\n
<\/spectrum><\/pre>\n
 PuTTY download<\/a> <\/p>\n","protected":false},"excerpt":{"rendered":"
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<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5,21],"tags":[],"class_list":["post-16","post","type-post","status-publish","format-standard","hentry","category-chemoinformatics","category-structure-elucidation"],"_links":{"self":[{"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/posts\/16"}],"collection":[{"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/comments?post=16"}],"version-history":[{"count":0,"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/posts\/16\/revisions"}],"wp:attachment":[{"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/media?parent=16"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/categories?post=16"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.steinbeck-molecular.de\/steinblog\/index.php\/wp-json\/wp\/v2\/tags?post=16"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}