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9th August 2013 @ 15:09

This post is compatible for submission to ChemSpider Reactions.

See ChemSpider Reactions template - help and further information for help when using it.

Reaction information

*#Reaction file
CSSP verscheme for 4_82.cdx
*Reaction file type CDX
*Procedure To a stirred suspension of Cp2ZrHCl (0.258 g, 1.0 mmol) in dry THF (10 mL) at RT was added neat 1-octene (0.125 mL, 0.8 mmol) dropwise over 3 minutes. After stirring the yellow solution for 1 h at RT, the reaction mixture was cooled to –78 C and a solution of the non-1-yn-3-yl benzensulfonate (0.294 g, 1.0 mmol) in dry THF (1 mL) was added dropwise followed by dropwise addition of freshly prepared LiTMP, [prepared from freshly distilled 2,2,6,6-tetramethylpiperidine (0.17 mL, 1.0 mmol) in dry THF (2 mL) and n-BuLi (0.4 mL of a 2.5 M solution in hexanes, 1.0 mmol) at –5 C over 15 min]. The stirring was continued for a further 1.5 h during which time the reaction mixture was allowed to warm to RT. The reaction mixture was re-cooled to –78 C and a solution of acetone (0.22 mL 3.0 mmol) in dry THF (1 mL) was added, the reaction mixture warmed gradually to RT. The reaction mixture was then refluxing for 20 h before cooling to RT and quenching with MeOH (5 mL) and a saturated aqueous solution of NaHCO3 (6 mL), the mixture left stirring overnight. The mixture was poured onto H2O (100 mL), the products extracted with Et2O (3 × 75 mL). The combined organic phases were washed with H2O (2 × 100 mL) and brine (100 mL), dried over MgSO4, filtered and concentrated in vacuo to give the crude product as a yellow oil. Purification of the crude material by column chromatography on SiO2 (230 – 400 mesh) with hexane : EtOAc (10 : 1) as the eluent to yield the title compound as a yellow oil in yield of 0.118 g (50%, contained 10% of unidentified by-products).
*Yield (%) 50
*Type of Yield Isolated product yield
Reference(s)
JS Thesis 10_08.12.09 Final VI_pp99-100.pdf
;
JS Thesis 10_08.12.09 Final VI_pp240-241.pdf
Further information Characterisation of rac-3-Hexyl-2-methyltridec-4-yn-2-ol (4.82d)

For multistep reactions (or their steps):

Overall reaction?  
For overall reaction - links to child reaction steps  
For step in multistep reaction - link to previous reaction step  
For step in multistep reaction - link to following reaction step  
9th August 2013 @ 14:15

About Template

This page contains additional information for the LabTrove ChemSpider Reactions template. LabTrove posts which are created using this template will be compatible for submission to ChemSpider Reactions

  • For more specific help about these fields and what to fill them with see the corresponding Help page
  • Fields marked * are mandatory
  • Fields marked # correspond to files - you will need to upload the data file into this LabTrove post, and when uploaded click on the "add link to text" button next to it to insert a link in the appropriate point of the template.

Help about fields in template

*#Reaction file File containing reaction - must be either a ChemDraw (.cdx) or RXN (.rxn) file or an RSMARTS string.
*Reaction file type Allowed values for reaction file type are:
  • CDX
  • RXN
  • RSMARTS
*Procedure Text description of procedure of reaction
*Yield (%) Yield of reaction in %. Does not need filling in if this is a step in a multistep reaction
*Type of Yield Definition of Yield supplied- e.g. Reaction Yield, Isolated Product Yield etc.
Further information Can be references of uploaded files or links to other pages related to this reaction (e.g. characterisation of compounds)

Multistep reactions - table only needs filling in for multistep reactions (or their steps)

Overall reaction? enter "true" if so, or "false" for a step in a multistep reaction
For overall reaction - links to child reaction steps Only fill in for reaction page describing overall definition of a multistep reaction
For step in multistep reaction - link to previous reaction step Only fill in for reaction page describing a constituent step in a multistep reaction
For step in multistep reaction - link to following reaction step Only fill in for reaction page describing a constituent step in a multistep reaction

Field to be populated automatically or when the deposition widget is activated:

  • URL of original source
Linked Posts
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5th June 2013 @ 17:32

For CSSP

  • author roles to be included
  • change "compound being made" to "compound(s) being made"
  • when you save it the save button disappears because it goes under the toolbox
  • if email address for an author is blank then don't include (Peter Scott suggested)

ChemSpider

  • allow "assignment of peaks" to be new field for spectra uploaded to ChemSpider
  • Need corresponding (image?) field to be added to show molecule with atoms labelled so that peak assignments make sense
  • scale spectra images that are big (see 29211612)
  • external links id gets lost
  • deal with v3000 mol files
  • weird characters in depositions don't go

For LabTrove

  • define metadata dropdown in template Artifact 3614188
  • allow default values, dropdown lists, checkboxes and dates to be specified for fields in templatesArtifact 3614189 - ammended to add hyperlinks, links to blog posts and uploadfiles too
  • "upload" box is awful!
  • "Reason for edit" field is annoying
Linked Posts
3rd June 2013 @ 14:06

Find a reaction, put the compound(s) made in it into LabTrove using the ChemSpider compound and associated data template and into ChemSpider (if it's a pure compound - not a mixture) and the reaction that produced it into LabTrove using the ChemSpider SyntheticPages style reaction template and into ChemSpider SyntheticPages.

Example post for J Stec's thesis: 

JS Thesis 10_08.12.09 Final VI.pdf
, compound 4.82d, and the reaction that forms it:

Putting compound data into LabTrove and ChemSpider:

  • ChemSpider ID can be found by doing a search on ChemSpider on the page http://www.chemspider.com/Search.aspx. Try a search on name first, and then structure if not.
  • Input into LabTrove:
    • Use ChemSpider compound and associated data template (with help page
    • title of post is name of compound followed by reference number
    • all data needs to be for pure compound (not mixture)
    • Spectra files - if it's for the compound (not a mixture etc.) then store it here. If so need to track down each source file, save it as a jcamp files (jdx/dx) and as a pdf and then upload these files into the page and put a link into the table for spectra
    • paste peak assignment text into Comments box for each spectrum
  • Input into ChemSpider:
    • Will be more instructions about this in training by ChemSpider curators
    • Click on Deposit Structuresin Depositions menu
    • load mol to deposit
    • External ID: is title of page in LabTrove formatted e.g. like: "Characterisation of rac-3-Hexyl-2-methyltridec-4-yn-2-ol (4.82d)" LabTrove ELN post
    • External URL: is the link to the LabTrove post
    • Description and Tags are just copied from fields with same names in LabTrove template
    • Identifiers are copied from Chemical Name, Common Name and Synonyms fields in LabTrove template

Putting reactions into LabTrove and ChemSpider/CSSP:

  • Input into LabTrove:
    • Submissions page is: http://cssp.chemspider.com/ArticleImport.aspx
    • Use ChemSpider SyntheticPages style reaction template (with help page
    • Author2 is whoever wrote the thesis
    • "Procedure or transformation" you’ll have to put together yourself – find nearest subtitle for inspiration, and include name of product to make it unique. Make it be the same as the title of this LabTrove post.
    • "Compound being made" – see if you can get it from the contents, or list of compounds at end, or failing all else use a structure to name generator once it has been drawn out. Mark it up as link to compound page in LabTrove.
    • "Chemicals used" from description of reaction, contents, list of compounds or name to structure generator (are supplier, concentration or purity available in lab notebook)? Do a ChemSpider search for each one and mark them up as a link to ChemSpider if so (with format e.g. http://www.chemspider.com/Chemical-Structure.28605365.html). If the compound is in chemspider but the name isn't there or approved then add it as a synonym. If the compound isn't in ChemSpider then add it.
    • "Procedure" copy from end section
    • "Authors Comments" from lab notebook?
    • "Lead reference" is thesis title unless it's been published somewhere 
    • "Data" - just put in types of spectra that characterised product
    • "Data file 1"etc. – for spectra for pure compounds (already loaded in compound characterisation page) then just put in links to data files already loaded up. If they haven't been loaded (for mixtures etc.) then upload the jdx file into this page and put a link to it in the boxes here. The 
    • Also pdf any relevant pages in the thesis and upload the files to the labtrove post (just at the end of it, no need to link in it)
    • watch out for weird symbols when pasted in (check how it looks once published)
    • to make the "Scheme" structure and image file, copy and paste the reaction from the thesis into ChemDraw CSSP template (
      CSSP.cds
      ), take out intermediates. Will be more instructions about this in training by ChemSpider curators
  • Input into CSSP: 
    • copy and paste from LabTrove post above into CSSP article import page
    • Some extra fields to manually make for now are:
    • Author1 is you
    • Abstracted submission field - original url will be to LabTrove post, and ID with be e.g. "Whitby group ELN LabTrove post ID 42193" (post ID viewable in url of post)
    • leave embargo field blank
    • Will be more instructions about this in training by ChemSpider curators

If you have any feature requests for CSSP, ChemSpider, or LabTrove add them to here: Feature requests

Attached Files
31st May 2013 @ 17:31

This post is compatible for submission to ChemSpider.

See ChemSpider compound and associated data template - help and further information for help when using it.

Compound

CSID 28605365
*#Compound mol file
jstec_4_82d.mol

Description and Tags

Description Compound 4.82d in J. Stec's thesis
Tags (separated by comma)  

Identifiers

*Chemical Name rac-3-Hexyl-2-methyltridec-4-yn-2-ol
Common Name  
Synonym  

Spectra

  *#Spectrum jcamp file *Spectrum Type Comments OpenData Image or PDF
Spectrum 1
nv1707jst2.010.001.jdx
HNMR 1H NMR (400 MHz, CDCl3): δ (ppm) = 2.34 (1H, m, H4), 2.20 (2H, td, J = 7.0, 2.0 Hz, H1), 1.97 (1H, br s, OH), 1.61 (1H, m), 1.54 – 1.47 (3H, m), 1.41 – 1.26 (18H, m), 1.25 (3H, s, H6/7), 1.24 (3H, s, H6/7), 0.90 (3H, t, J = 6.8 Hz, H13/20), 0.89 (3H, t, J = 6.8 Hz, H13/20) Y
nv1707jst2.010.001.jdx
Spectrum 2
nv1707jst2.011.001.jdx
CNMR 13C NMR (100.5 MHz, CDCl3): δ (ppm) = 84.33 (C2), 80.35 (C3), 71.98 (C5), 45.34 (CH4), 31.81 (2CH2), 30.07 (CH2), 29.21 (CH2), 29.14 (CH2), 29.07 (2CH2), 28.84 (CH2), 28.36 (CH2), 27.01 (CH36/7), 26.24 (CH36/7), 22.63 (2CH2), 18.70 (CH21), 14.06  (2CH313 + 20) Y
nv1707jst2.011.001.JPG
Spectrum 3
nv1707jst2.012.001.jdx
CNMR 13C NMR (100.5 MHz, CDCl3): δ (ppm) = 84.33 (C2), 80.35 (C3), 71.98 (C5), 45.34 (CH4), 31.81 (2CH2), 30.07 (CH2), 29.21 (CH2), 29.14 (CH2), 29.07 (2CH2), 28.84 (CH2), 28.36 (CH2), 27.01 (CH36/7), 26.24 (CH36/7), 22.63 (2CH2), 18.70 (CH21), 14.06  (2CH313 + 20) Y
nv1707jst2.012.001.JPG
Spectrum 4
nv1707jst2.013.001.jdx
CNMR 13C NMR (100.5 MHz, CDCl3): δ (ppm) = 84.33 (C2), 80.35 (C3), 71.98 (C5), 45.34 (CH4), 31.81 (2CH2), 30.07 (CH2), 29.21 (CH2), 29.14 (CH2), 29.07 (2CH2), 28.84 (CH2), 28.36 (CH2), 27.01 (CH36/7), 26.24 (CH36/7), 22.63 (2CH2), 18.70 (CH21), 14.06  (2CH313 + 20) Y
nv1707jst2.013.001.JPG
Spectrum 5   Electron Impact HRMS (EI): Found: [M – CH3]+, 279.2694. [C19H35O]+ requires: 279.2688 Y  
Spectrum 6   Chemical Ionization +ve LRMS (CI): m/z: 294 ([M]+, 26%), 277 ([M – H2O + H]+, 100 %) Y  
Spectrum 7   Chemical Ionization +ve LRMS (CI): m/z: 294 ([M]+, 26%), 277 ([M – H2O + H]+, 100 %) Y  
Spectrum 8   2D NMR 1H-13C Long-range correlation   Y
hmbc
 

Properties

Experimental Physico-chemical Properties

Property Value Unit Comments
Experimental Boiling Point      
Experimental Flash Point      
Experimental Freezing Point      
Experimental Gravity      
Experimental Ionization Potent      
Experimental LogP      
Experimental Melting Point      
Experimental Optical Rotation      
Experimental Refraction Index      
Experimental Solubility      
Experimental Vapor Pressure      
Non Water Solubility      
Non Water Solubility      

Spectroscopy

Property Value Unit Comments
Lambda Max      

Miscellaneous

Property Value Unit Comments
Appearance yellow oil    
Bio Activity      
Chemical Class      
Compound Source      
Drug Status      
Exposure Limits      
Exposure Limits Niosh Rel      
Exposure Routes      
First-Aid      
Incompatability      
Personal Protection      
Safety      
Stability      
Symptoms      
Target Organs      
Therapeutical Effect      
Toxicity      
Linked Posts
Attached Files