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Topic: Silicon-carbon compound chemistry  (Read 8096 times)

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Nucleophile

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Silicon-carbon compound chemistry
« on: June 29, 2005, 11:05:14 AM »
I wasn't sure where the silicon chemists hang out so I posted it here. :)

Here's the deal. I am writing this paper on Catalytical antibodies, as a part of which I need to propose a so-called "Transition State Analogue", a stable molecule which resembles in electronic and geometric terms, the rate determining transition state of the reaction I intend to catalyse. See some of this stuff below:

Nucleophile

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Re:Silicon-carbon compound chemistry
« Reply #1 on: June 29, 2005, 11:09:16 AM »
My question is, is there some compund to create a silyl ether like that?

For example, can I react something like Si(Me)2Cl2 with an alcohol, to get this, and then add some water for the OH group to replace the remaining Chloride?

and if so will the pKa of the silyl alcohol be low enough to be deprotonated at pH~7?
and if not will I be able to use Germanium instead, perhaps?

I know these are a lot of questions, but it's a reflection of my musing on the issue in the last couple of weeks.

Offline DrCMS

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Re:Silicon-carbon compound chemistry
« Reply #2 on: June 30, 2005, 04:13:08 AM »
You should have posted this in the organic section.

Why do you think this silicon compound will be any more stable than the carbon intermediate?  

Si-O is the 2nd strongest covalent bond going, if you add dichlorodimethylsilane to and alcohol it will react at both Si-Cl bonds.

The geometry around a silicon centre will not be identical to a carbon due to the difference in bond lengths etc.

All in all this is intermediate will not be stable and will not have the same geometry as the one you're interested in.

Nucleophile

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Re:Silicon-carbon compound chemistry
« Reply #3 on: June 30, 2005, 08:49:03 AM »
My line of reasoning:

-Silyl ethers are relatively stable.
-the O- will be a result of a natural deprotonation in an aqueous solution at pH7: that is, if the proton is acidic enough ( which was one of my questions)

GCT

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Re:Silicon-carbon compound chemistry
« Reply #4 on: June 30, 2005, 01:05:13 PM »
It seems that you've got quite an unstable TSA, tertiary intermediate...

Nucleophile

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Re:Silicon-carbon compound chemistry
« Reply #5 on: June 30, 2005, 01:27:30 PM »
What exactly makes the TSA unstable?

cbee

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Re:Silicon-carbon compound chemistry
« Reply #6 on: June 30, 2005, 04:09:08 PM »
Siyloxide anion will not be deprotonated at ph=7.  Silicon is significantly more electropositive than carbon so this proton will be less acidic than the corresponding carbon analog.  If (using a suitlably strong base) you did deprotonate this species, the resulting anion would be too reactive to be useful.


Cisco

Nucleophile

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Re:Silicon-carbon compound chemistry
« Reply #7 on: June 30, 2005, 05:01:06 PM »
Yes, true, but IIRC, Si-OH on the surface of silica is acidic...

Damn, I've just realized how little about the chemistry of Silicon I know.

EDIT: besides, isn't electronegativity first and foremost about sigma donation? IIRC, Silicon is a pi-acceptor, and thus Si-OH can be acidic.
« Last Edit: June 30, 2005, 05:25:06 PM by Nucleophile »

cbee

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Re:Silicon-carbon compound chemistry
« Reply #8 on: June 30, 2005, 05:55:27 PM »
Silica is very mildly acidic.  The problem is that you need something that will exist in anionic form at pH7 which this species will not.

Also, I'm not sure (and I could be wrong, I can't remember this stuff too well) that Si is a good pi acceptor.  Don't you need a vacant pi orbital for this?  You have no pi* or pi orbitals period in the valence shell, empty or not, in hybridized silicon, do you?  Anyway, even if you do allow back bonding, while often important, does not usually overide strong sigma bond effects, does it?  I'm not saying that this hydrogen is not acidic at all, just not to the degree you require.  Have you thought of something like florine?  You won't get the naked anion, but it is electronegative.

Cisco

Offline Dude

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Re:Silicon-carbon compound chemistry
« Reply #9 on: June 30, 2005, 06:07:07 PM »
Silanols (Si-OH) and silanolates (Si-O - ) are known compounds and intermediates.  Silanolates have a strong tendency to polymerize to siloxanes.  There is a somewhate dated but comprehensive book on silicon chemistry by Eaborn.  The problem I see with your picture is specificity and stability.  

1.  It is unlikely that one alcohol will preferentially react and leave the other intact (based upon your picture).
2.   An excess of dichlorodimethylsilane will react with an alcohol to generate HCl and two terminal chloroalkoxysilane groups.  Converting them into the silanolate anions while still attached to the organic group will be tricky.  Although very thermally stable, alkoxysilanes are water sensitive and are easily cleaved from the organic portion by either acid or base (hence the silicon based protecting groups in alcohol chemistry that are typically acid cleaved).  

Nucleophile

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Re:Silicon-carbon compound chemistry
« Reply #10 on: July 01, 2005, 01:49:09 AM »
cbee: I am not sure about the Siloxane being deprotonated -but I've seen it's pKA placed at around 6.

Dude: no, the Fluorine isn't enough ( way ahead of you ;) ) I've specifically proposed this, but the professor sez that you have got to have a counter charged amino-acid near it, not partial charge.

Nucleophile

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Re:Silicon-carbon compound chemistry
« Reply #11 on: July 02, 2005, 02:37:12 AM »
Thanks for all the help, guys. I've decided to use a somewhat larger protective group ( a larger ketone), and use an N-oxide there.

I just did  the preliminary lecture on that yesterday, and it went just fine.

« Last Edit: July 02, 2005, 02:45:45 AM by Nucleophile »

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