teaching nmr spectroscopy using online resources from rsc

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DESCRIPTION

The Royal Society of Chemistry hosts an online resource, ChemSpider, as a structure centric database for chemists linking over 25 million chemicals to 400 internet sites. As a crowdsourced environment members of the chemistry community can deposit spectral data to the database. Almost 2000 NMR spectra have been submitted to the database and these are the basis of both a gaming environment for learning NMR spectroscopy, the SpectralGame, as well as a new teaching environment known as SpectraSchool. This presentation will provide an overview of these two online resources and how they may be utilized for the purpose of teaching NMR spectroscopy in an Undergraduate Curriculum.

TRANSCRIPT

Teaching NMR spectroscopy using online resources from the

Royal Society of Chemistry

Antony J Williams, Alexey Pshenichnov, Valery Tkachenko and Richard Oakley

ACS San Diego March 2012

NMR Spectroscopy on the Internet Presentations, tutorials and guidance Tables of information Spectral data for download Assigned NMR spectra – tables NMR prediction algorithms – free and commercial

RSC is working hard on Spectroscopy….

RSC Spectroscopy Resources

ChemSpider for storing spectral data > 2000 spectra (www.chemspider.com)

ChemSpider serving up data for the SpectralGame (www.spectralgame.com)

SpectraSchool for learning about interpreting spectra. Not just NMR (http://spectraschool.rsc.org/)

MORE planned…

http://www.chemspider.com/

http://www.spectralgame.com/

http://spectraschool.rsc.org/

ChemSpider

27 million chemicals with associated data…

http://www.chemspider.com/

http://www.chemspider.com/About.aspx?

http://www.chemspider.com/About.aspx

http://www.chemspider.com/Sponsors.aspx

http://www.chemspider.com/Search.aspx?

http://www.chemspider.com/Search.aspx

http://www.chemspider.com/History.aspx

http://www.chemspider.com/AboutServices.aspx?

http://www.chemspider.com/Help.aspx?

http://www.chemspider.com/FAQ.aspx

http://www.chemspider.com/SiteMap.aspx

http://www.chemspider.com/StructureSearch.aspx

http://www.chemspider.com/FullSearch.aspx

Cholesterol on ChemSpider

http://www.chemspider.com/About.aspx

http://www.chemspider.com/Sponsors.aspx

http://www.chemspider.com/Search.aspx

http://www.chemspider.com/History.aspx

http://www.chemspider.com/FAQ.aspx

http://www.chemspider.com/SiteMap.aspx

http://www.chemspider.com/FilesHandler.ashx?type=str&striph=yes&id=5775

http://www.chemspider.com/Chemical-Structure.5775.html

http://www.chemspider.com/Molecular-Formula/C27H46O

http://www.chemspider.com/Chemical-Structure.5775.html?rid=4a955592-0622-43ec-ad9c-ce5d383886db

http://www.chemspider.com/Chemical-Structure.5775.html?rid=4a955592-0622-43ec-ad9c-ce5d383886db

http://www.google.com/search?q=InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1

http://www.google.com/search?q=HVYWMOMLDIMFJA

http://www.google.com/search?q=HVYWMOMLDIMFJA-DPAQBDIFSA-N

http://www.chemspider.com/Chemical-Structure.5775.html?rid=4a955592-0622-43ec-ad9c-ce5d383886db

http://www.chemspider.com/Chemical-Structure.5775.html?rid=4a955592-0622-43ec-ad9c-ce5d383886db

ChemSpider : Spectra Linked

http://rainier.chem.plu.edu/nutsform.html

http://www.chemspider.com/UserProfile.aspx?usr_id=181

http://opendefinition.org/

http://rainier.chem.plu.edu/nutsform.html

http://www.chemspider.com/UserProfile.aspx?usr_id=181

http://opendefinition.org/

http://webbook.nist.gov/cgi/cbook.cgi?ID=C57885&Units=SI&Mask=200

http://www.chemspider.com/UserProfile.aspx?usr_id=181

Spectra Linked

Spectra Linked

Sources of Spectra

Sourced from online sources with permission

Private collections

The MAJORITY deposited by ChemSpider users

Spectral Uploading

Locate the structure of interest and deposit spectrum

http://www.chemspider.com/UpdateBox.aspx?id=1020&type=synonym

http://www.chemspider.com/UpdateBox.aspx?id=1020&type=description

http://www.chemspider.com/AddBlob.aspx?id=1020&type=image

http://www.chemspider.com/AddBlob.aspx?id=1020&type=spectrum

http://www.chemspider.com/AddBlob.aspx?id=1020&type=cif

http://www.chemspider.com/UpdateBox.aspx?id=1020&type=datasources

Spectral Uploading Various types of NMR spectra supported

Regular Updates

http://www.chemspider.com/Chemical-Structure.9496156.html

http://www.chemspider.com/Chemical-Structure.7630.html

http://www.chemspider.com/Chemical-Structure.7630.html

http://www.chemspider.com/Chemical-Structure.11286815.html

Multiple Spectra for One Structure

ChemSpider ID 24528095 H1 NMR

ChemSpider ID 24528095 C13 NMR

ChemSpider ID 24528095 HHCOSY

ChemSpider ID 24528095 HSQC

ChemSpider ID 24528095 HMBC

Full C13 assignment uploaded

Available Spectra http://www.chemspider.com/spectra.aspx

Embedding Data

Learn Chemistry Wiki

http://www.rsc.org/

http://pubs.rsc.org/

http://www.chemspider.com/

http://my.rsc.org/

http://www.rsc.org/learn-chemistry/wiki/Main_Page

http://www.rsc.org/learn-chemistry

http://www.rsc.org/learn-chemistry/wiki/Main_Page

http://www.rsc.org/learn-chemistry/wiki/Lab:Experiments

http://www.rsc.org/learn-chemistry/wiki/Quiz:Overview

http://www.rsc.org/learn-chemistry/wiki/Tutorials_and_guides

http://www.rsc.org/learn-chemistry/wiki/Substance:Overview

http://www.rsc.org/learn-chemistry

http://www.rsc.org/learn-chemistry/wiki

http://www.rsc.org/learn-chemistry/wiki/index.php?title=Special:UserLogin&returnto=Main_Page

http://www.rsc.org/learn-chemistry/wiki/Main_Page

http://www.rsc.org/learn-chemistry/wiki/index.php?title=Talk:Main_Page&action=edit&redlink=1

http://www.rsc.org/learn-chemistry/wiki/index.php?title=Main_Page&action=edit

http://www.rsc.org/learn-chemistry/wiki/index.php?title=Main_Page&action=history

http://www.rsc.org/learn-chemistry/wiki/Overview

http://www.rsc.org/learn-chemistry/wiki/Site_tour

http://youtu.be/ynR53htri60

http://www.rsc.org/learn-chemistry/wiki/Introductory_and_general_chemistry

http://www.rsc.org/learn-chemistry/wiki/Organic_chemistry

http://www.rsc.org/learn-chemistry/wiki/Inorganic_chemistry

http://www.rsc.org/learn-chemistry/wiki/Physical_and_theoretical_chemistry

http://www.rsc.org/learn-chemistry/wiki/Biochemistry

http://www.rsc.org/learn-chemistry/wiki/Analytical_chemistry

http://www.rsc.org/learn-chemistry/wiki/Analytical_science

http://www.rsc.org/learn-chemistry/wiki/Catalysis

http://www.rsc.org/learn-chemistry/wiki/Computational_chemistry

http://www.rsc.org/learn-chemistry/wiki/Supramolecular_chemistry_and_nanoscience

http://www.rsc.org/learn-chemistry/wiki/Materials_chemistry

http://www.rsc.org/learn-chemistry/wiki/Synthesis

http://www.rsc.org/learn-chemistry/wiki/Green_and_environmental_chemistry

http://www.rsc.org/learn-chemistry/wiki/Projects_and_collaborations

http://www.rsc.org/learn-chemistry/wiki/Substance:Overview

http://www.rsc.org/learn-chemistry/wiki/Lab:Experiments

http://www.rsc.org/learn-chemistry/wiki/Quiz:Overview

http://www.rsc.org/learn-chemistry/wiki/Tutorials_and_guides

http://www.rsc.org/learn-chemistry/wiki/Community_portal

http://www.rsc.org/learn-chemistry/wiki/Overview

http://www.rsc.org/learn-chemistry/wiki/File:MainImageMapSep8_2011_800px.png

http://www.rsc.org/learn-chemistry/wiki/Main_Page

http://www.rsc.org/learn-chemistry/wiki/Learn_Chemistry_Wiki:Community_portal

http://www.rsc.org/learn-chemistry/wiki/Learn_Chemistry_Wiki:Current_events

http://www.rsc.org/learn-chemistry/wiki/Special:RecentChanges

http://www.rsc.org/learn-chemistry/wiki/Special:Random

http://www.rsc.org/learn-chemistry/wiki/Help:Contents

http://www.rsc.org/learn-chemistry/wiki/Report_error

http://www.rsc.org/learn-chemistry/wiki/Special:WhatLinksHere/Main_Page

http://www.rsc.org/learn-chemistry/wiki/Special:RecentChangesLinked/Main_Page

http://www.rsc.org/learn-chemistry/wiki/Special:SpecialPages

http://www.rsc.org/learn-chemistry/wiki/index.php?title=Main_Page&printable=yes

http://www.rsc.org/learn-chemistry/wiki/index.php?title=Main_Page&oldid=22900

Learn Chemistry Wiki Substances

http://www.rsc.org/learn-chemistry/wiki/Substance:List_of_substances

http://www.rsc.org/learn-chemistry/wiki/Substance:A

http://www.rsc.org/learn-chemistry/wiki/Substance:B

http://www.rsc.org/learn-chemistry/wiki/Substance:C

http://www.rsc.org/learn-chemistry/wiki/Substance:D

http://www.rsc.org/learn-chemistry/wiki/Substance:E

http://www.rsc.org/learn-chemistry/wiki/Substance:F

http://www.rsc.org/learn-chemistry/wiki/Substance:GH

http://www.rsc.org/learn-chemistry/wiki/Substance:I

http://www.rsc.org/learn-chemistry/wiki/Substance:JKL

http://www.rsc.org/learn-chemistry/wiki/Substance:M

http://www.rsc.org/learn-chemistry/wiki/Substance:N

http://www.rsc.org/learn-chemistry/wiki/Substance:OP

http://www.rsc.org/learn-chemistry/wiki/Substance:QR

http://www.rsc.org/learn-chemistry/wiki/Substance:S

http://www.rsc.org/learn-chemistry/wiki/Substance:T

http://www.rsc.org/learn-chemistry/wiki/Substance:UVW

http://www.rsc.org/learn-chemistry/wiki/Substance:XYZ

http://www.ggasoftware.com/

Learn Chemistry Wiki Substances

Learn Chemistry Wiki Substances

http://www.chemspider.com/Chemical-Structure.2991.html

http://msds.chem.ox.ac.uk/BE/benzophenone.html

http://www.chemspider.com/Spectrum.aspx?spc_id=929

http://www.chemspider.com/Spectrum.aspx?spc_id=1223

http://www.chemspider.com/Spectrum.aspx?spc_id=930

http://www.chemspider.com/Spectrum.aspx?spc_id=1143

http://www.nmrshiftdb.org/portal/js_pane/P-Results/nmrshiftdbaction/showDetailsFromHome/molNumber/10005796

http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng

http://www.chemspider.com/AddBlob.aspx?id=2991&type=spectrum

http://www.rsc.org/learn-chemistry/wiki/Help:How_to_add_new_spectra

http://en.wikipedia.org/wiki/organic%20compound

http://en.wikipedia.org/wiki/carbon

http://en.wikipedia.org/wiki/hydrogen

http://en.wikipedia.org/wiki/oxygen

http://en.wikipedia.org/wiki/phenyl

http://en.wikipedia.org/wiki/Benzophenone

http://en.wikipedia.org/w/index.php?title=Benzophenone&action=edit

Learn Chemistry Wiki Substances

http://www.chemspider.com/Chemical-Structure.2991.html

http://msds.chem.ox.ac.uk/BE/benzophenone.html

http://www.chemspider.com/Spectrum.aspx?spc_id=929

http://www.chemspider.com/Spectrum.aspx?spc_id=1223

http://www.chemspider.com/Spectrum.aspx?spc_id=930

http://www.chemspider.com/Spectrum.aspx?spc_id=1143

http://www.nmrshiftdb.org/portal/js_pane/P-Results/nmrshiftdbaction/showDetailsFromHome/molNumber/10005796

http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng

http://www.chemspider.com/AddBlob.aspx?id=2991&type=spectrum

http://www.rsc.org/learn-chemistry/wiki/Help:How_to_add_new_spectra

http://en.wikipedia.org/wiki/organic%20compound

http://en.wikipedia.org/wiki/carbon

http://en.wikipedia.org/wiki/hydrogen

http://en.wikipedia.org/wiki/oxygen

http://en.wikipedia.org/wiki/phenyl

http://en.wikipedia.org/wiki/Benzophenone

http://en.wikipedia.org/w/index.php?title=Benzophenone&action=edit

Learn Chemistry Wiki Substances

http://usefulchem.wikispaces.com/Exp093

http://www.chemspider.com/UserProfile.aspx?usr_id=182

NMRShiftDB: http://www.ebi.ac.uk/nmrshiftdb/

Learn Chemistry Wiki Substances

http://nmrshiftdb.nmr.uni-koeln.de/portal/js_pane/P-Help;jsessionid=CF032E5D7370A3EB5AB3AA954FA2D22B?URL=using.html

http://nmrshiftdb.nmr.uni-koeln.de/portal/js_pane/P-Results/nmrshiftdbaction/showDetailsFromHome/molNumber/10005796;jsessionid=CF032E5D7370A3EB5AB3AA954FA2D22B?$data.getRequest().getQueryString()&applet=applet&molNumber=10005796

http://nmrshiftdb.nmr.uni-koeln.de/portal/js_pane/P-Results/nmrshiftdbaction/showDetailsFromHome/molNumber/10005796;jsessionid=CF032E5D7370A3EB5AB3AA954FA2D22B?$data.getRequest().getQueryString()&applet=applet&molNumber=10005796

http://nmrshiftdb.nmr.uni-koeln.de/portal/js_pane/P-Help;jsessionid=CF032E5D7370A3EB5AB3AA954FA2D22B?URL=using.html

http://nmrshiftdb.nmr.uni-koeln.de/portal/js_pane/P-Results/nmrshiftdbaction/showDetailsFromHome/molNumber/10005796;jsessionid=CF032E5D7370A3EB5AB3AA954FA2D22B?$data.getRequest().getQueryString()&applet=applet&molNumber=10005796

http://nmrshiftdb.nmr.uni-koeln.de/portal/js_pane/P-Results/nmrshiftdbaction/showDetailsFromHome/molNumber/10005796;jsessionid=CF032E5D7370A3EB5AB3AA954FA2D22B?$data.getRequest().getQueryString()&applet=applet&molNumber=10005796

http://nmrshiftdb.nmr.uni-koeln.de/portal;jsessionid=CF032E5D7370A3EB5AB3AA954FA2D22B

http://nmrshiftdb.nmr.uni-koeln.de/portal;jsessionid=CF032E5D7370A3EB5AB3AA954FA2D22B

Where do data come from?

ChemSpider users deposit data Some contributions from NIST Chemical vendors are starting to provide data.

Synthonix are one of our major contributors (www.synthonix.com)

http://synthonix.com/

http://synthonix.com/catalogsearch/advanced/

http://synthonix.com/buy-online/s-t/spiro-compounds.html

http://synthonix.com/buy-online/a-b/azetidines.html

http://synthonix.com/buy-online/o-p/oxetanes.html

Web Services

http://www.chemspider.com/Spectra.asmx?WSDL

http://www.chemspider.com/Spectra.asmx?op=GetAllSpectraInfo

http://www.chemspider.com/Spectra.asmx?op=GetCompoundSpectraInfo

http://www.chemspider.com/Spectra.asmx?op=GetSpectraInfoArray

http://www.chemspider.com/Spectra.asmx?op=GetSpectrumInfo

www.SpectralGame.comhttp://www.jcheminf.com/content/1/1/9

http://www.spectralgame.com/

Spectral Game

Increasing Complexity

SpectralGame in the hand

An open-source and free HTML5 toolkit. For desktop and mobile browsers.

ChemDoodle Web Components

SpectraSchool http://spectraschool.rsc.org/

http://spectraschool.rsc.org/

SpectraSchool Videos

SpectraSchool

SpectraSchool

http://www.rsc.org/

http://spectraschool.rsc.org/

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Video

http://www.rsc.org/sias

http://spectraschool.rsc.org/Help

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Help/Helpers/

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

Identify Mode

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

http://spectraschool.rsc.org/Spectra

Spectroscopy in a Suitcase

Invitations

Spectral data are welcomed from associated syntheses, lab experiments etc

Upload structures, spectra, analyses etc to ChemSpider to share with the community

Use www.SpectralGame.com and encourage your students

Coming Soon Storage and display of ASSIGNED spectra

Acknowledgments Alexey Pshenichnov, University of Leicester and Richard Oakley –

SpectraSchool

Aileen Day and Martin Walker – Learn Chemistry Wiki

Jean-Claude Bradley, Andrew Lang, Robert Lancashire, Kevin Thiesen (ChemDoodle) – SpectralGame

Gary Allred and Chi Wang – Synthonix Data

Ryan Sasaki, Sergey Golotvin, Pranas Japertas ACD/Labs –Bulk data processing and Display Widget

Depositors of data – there are many!

Thank you

Email: williamsa@rsc.org Twitter: ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams

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