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1st July 2013 @ 15:32

This post is compatible for submission to ChemSpider SyntheticPages.

See ChemSpider SyntheticPages style reaction template - help and further information for help when using it.

SOURCE

Author 1 is the author of this LabTrove post (and has contributor role of "Abstracter").

  *First name *Last name Email Organization Role
Author 2 Józef Stec   University of Southampton Doer
Author 3 Richard Whitby   University of Southampton Conceiver
Author 4          

TEXT

*Procedure or Transformation Access to a trans-pentalene structure via, Insertion of dihalocarbenoids and acetylides into zirconacyclopentanes: rac-((3aR,6aR)-Octahydro-2,2-bis(methoxymethyl)-5-(1-phenylvinyl)-pentalen-5-yl)dimethyl(phenyl)silane
*Compound(s) being made rac-((3aR,6aR)-Octahydro-2,2-bis(methoxymethyl)-5-(1-phenylvinyl)-pentalen-5-yl)dimethyl(phenyl)silane
*Chemicals used (delimited by semicolons ;) 4,4-Bis(methoxymethyl)hepta-1,6-dieneCp2ZrCl2; n-BuLi; (dichloromethyl)dimethyl(phenyl)silane; LDA; lithium phenylacetylide; MeOH; NaHCO3
*Procedure To a solution of Cp2ZrCl2 (0.293 g, 1.0 mmol) in dry THF (5 mL) cooled to –78 °C was added n-BuLi (0.80 mL of a 2.5 M solution in hexanes, 2.0 mmol) dropwise over 3 minutes. After 25 min at the same temperature, a solution of bis(methoxymethyl)hepta-1,6-diene (0.184 g, 1.0 mmol) in dry THF (3 mL) was added dropwise. After 30 min at -78 °C the reaction mixture was allowed to warm to room temperature and stirred for 2 h. After cooling the reaction mixture to –78 °C, a solution of (dichloromethyl)dimethyl(phenyl)silane (0.285 g, 1.3 mmol) in dry THF (1 mL) was added followed by dropwise addition of LDA (0.85 mL of a 1.8 M solution, 1.5 mmol). The reaction mixture was stirred for 0.5 h during which time was allowed to warm to –60 °C before re-cooling to –78 °C and dropwise addition of lithium phenyl acetylide, [prepared from phenylacetylene (0.33 mL, 3.0 mmol) in dry THF (3 mL) and n-BuLi (1.2 mL of a 2.5 M solution in hexanes, 3.0 mmol) at –5 °C over 15 min]. The stirring was continued for 3 h during which the reaction mixture was allowed to warm to –15 °C before addition of MeOH (5 mL) and a saturated aqueous solution of NaHCO3 (6 mL). The whole mixture was allowed to warm to room temperature and 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 (3 × 100 mL) and brine (100 mL), dried over MgSO4, filtered and concentrated in vacuo to give the crude product as a red oil. Purification of the crude material by column chromatography on SiO2 (230 – 400 mesh) with 2.5% of EtOAc in hexanes as the eluent gave the title compound as a yellow oil in yield of 0.152 g (35%).
*Authors Comments

This protocol has been used with a number of different acetylides and dihalocarbenoids, for example,

A modified approach - using LiTMP and 1,1-dibromoheptane to generate the lithated insertion species (step ii) and using lithium phenylacetylide (step iii) gave access to rac-(3aS,6aS)-2-Hexyl-octahydro-5,5-bis(methoxymethyl)-2-(1-phenylvinyl)pentalene in 77% yield.

Using LiTMP and 1,1-dibromoheptane to generate the lithated insertion species (step ii) and using 1-Octyn-1-yl lithium (step iii) gave access to rac-(3aS,6aS)-2-Hexyl-octahydro-5,5-bis(methoxymethyl)-2-(oct-1-en-2-yl)pentalene in 47% yield. 

Lead Reference Taken from thesis: J. Stec, 2009, "Tandem Reaction Sequences on a Zirconocene Template",PhD thesis, University of Southampton. Pages 79-81, 194-196
Other References  
Multimedia Content  
*Data 1H NMR (400 MHz, CDCl3); 13C NMR (100.5 MHz, CDCl3)
#Data file 1
H NMR - ma2708jst1.010.001.1r.jdx
#Data file 2
C NMR 0.14.jdx
#Data file 3  
#Data file 4  
#Data file 5  

SCHEME

*#Structure file (ChemDraw, ChemSketch or RXN file)
reaction scheme 3.34c.cdx
*#Image file (GIF or PNG)
reaction scheme 3.34c.gif

Keywords

Compounds Keywords Carbocyclic compound
Reactions Keywords Insertion 
Other Keywords  
Attached Files
1st July 2013 @ 15:28

This post is compatible for submission to ChemSpider SyntheticPages.

See ChemSpider SyntheticPages style reaction template - help and further information for help when using it.

SOURCE

Author 1 is the author of this LabTrove post (and has contributor role of "Abstracter").

  *First name *Last name Email Organization Role
Author 2 Jozef Stec   University of Southampton   Doer
Author 3 Richard Whitby   University of Southampton  Conceiver
Author 4          

TEXT

*Procedure or Transformation Allenyl carbenoid insertion into organochlorozirconocenes.
*Compound(s) being made rac-(1R,2R)-2-Methyl-1-phenyldodec-3-yn-1-ol
*Chemicals used (delimited by semicolons ;) Cp2ZrHCl; dry THF; neat 1-octenebut-3-yn-2-yl benzensulfonate; freshly distilled 2,2,6,6-tetramethylpiperidinen-BuLibenzaldehydeMeOHNaHCO3H2OEt2O; Brine; MgSO4EtOAc
*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 but-3-yn-2-yl methylbenzenesulfonate (0.224 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 h during which time the reaction mixture was allowed to warm to RT. The reaction mixture was re-cooled to –60 °C and a solution of benzaldehyde (0.30 mL, 3.0 mmol) in dry THF (1 mL) was added. The reaction mixture was warmed gradually to RT. The stirring was continued at the same temperature for 3 h before 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 yellow oil (anti : syn diastereoisomers in the ratio of of 74 : 26).

Purification of the crude material by careful column chromatography on SiO2 (230-400 mesh) with hexane : EtOAc (10 : 1) as the eluent to allow partial separation of the diasteroisomers to give a pure fraction of the title compound (anti isomer) as a yellow oil and a mixed fraction (yellow oil) of both isomers in combined yield of 0.130 g (60%).

*Authors Comments Hydrozirconation of 1-octene or 1-octyne with Schwartz reagent provides the organochlorozirconocene complex which then undergoes insertion of allenyl carbenoid to provide the ‘ate’ complex. Subsequent 1,2-metallate rearrangement gives the allenic zirconium intermediate which can be further elaborated through aldehyde and ketone insertion to provide secondary and tertiary alcohols respectively.
Lead Reference  J. Stec, 2009, "Tandem Reaction Sequences on a Zirconocene Template",PhD thesis, University of Southampton
Other References  -
Multimedia Content  -
*Data  1H NMR; 13C NMR; HRMS (EI); LRMS (CI); IR (thin film)
#Data file 1
H NMR of Product
 
#Data file 2
C NMR Product
#Data file 3  
#Data file 4  
#Data file 5  

SCHEME

Reaction Scheme (ChemDraw)
Reaction Scheme 4.82a.cdx
Reaction Scheme (Image)
Reaction Scheme 4.82a.png

Keywords

Compounds Keywords Alkanes; Alkenes; Alcohols; Aromatic/Arenes; Alkynes  
Reactions Keywords Insertion 
Other Keywords  
Attached Files
5th June 2013 @ 16:32

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 @ 13:06

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